VP13D_HUMAN
ID VP13D_HUMAN Reviewed; 4388 AA.
AC Q5THJ4; J3KP14; Q58F10; Q6MZK9; Q6ZV12; Q709C4; Q709C5; Q86UB4; Q9NSJ3;
AC Q9UIM0;
DT 28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Intermembrane lipid transfer protein VPS13D {ECO:0000305};
DE AltName: Full=Vacuolar protein sorting-associated protein 13D;
GN Name=VPS13D {ECO:0000312|EMBL:CAE75586.1, ECO:0000312|HGNC:HGNC:23595};
GN Synonyms=KIAA0453 {ECO:0000312|EMBL:BAA32298.3};
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1] {ECO:0000305, ECO:0000312|EMBL:CAE75586.1}
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), AND TISSUE SPECIFICITY.
RC TISSUE=Lymphoblast {ECO:0000269|PubMed:15498460};
RX PubMed=15498460; DOI=10.1016/j.ygeno.2004.04.012;
RA Velayos-Baeza A., Vettori A., Copley R.R., Dobson-Stone C., Monaco A.P.;
RT "Analysis of the human VPS13 gene family.";
RL Genomics 84:536-549(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
RN [3] {ECO:0000305, ECO:0000312|EMBL:CAB82724.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-2270.
RA Rhodes S., Huckle E.;
RL Submitted (DEC-1999) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000305, ECO:0000312|EMBL:BAA32298.3}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1179-4388 (ISOFORM 1).
RC TISSUE=Brain {ECO:0000312|EMBL:BAA32298.3};
RX PubMed=9455484; DOI=10.1093/dnares/4.5.345;
RA Seki N., Ohira M., Nagase T., Ishikawa K., Miyajima N., Nakajima D.,
RA Nomura N., Ohara O.;
RT "Characterization of cDNA clones in size-fractionated cDNA libraries from
RT human brain.";
RL DNA Res. 4:345-349(1997).
RN [5] {ECO:0000305, ECO:0000312|EMBL:BAC86054.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2039-3635 (ISOFORM 2).
RC TISSUE=Tongue {ECO:0000312|EMBL:BAC86054.1};
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2094-4388 (ISOFORM 2).
RC TISSUE=Fetal kidney;
RX PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D.,
RA Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A.,
RA Wiemann S., Schupp I.;
RT "The full-ORF clone resource of the German cDNA consortium.";
RL BMC Genomics 8:399-399(2007).
RN [7] {ECO:0000305, ECO:0000312|EMBL:AAH51804.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2980-4388.
RC TISSUE=Testis {ECO:0000312|EMBL:AAH51804.1};
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-1761, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-1761 AND SER-2435, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [10]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-3524, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C.,
RA Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1042, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2435, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T.,
RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.;
RT "System-wide temporal characterization of the proteome and phosphoproteome
RT of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-663; SER-1034; SER-1038;
RP SER-1042; SER-1138; SER-1598; SER-1603; SER-1699; THR-1761; SER-2671;
RP SER-2861; SER-2864 AND SER-2983, AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-663; SER-1138; SER-1341;
RP THR-1761; SER-1765 AND SER-2671, AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [15]
RP FUNCTION, AND DOMAIN.
RX PubMed=29307555; DOI=10.1016/j.cub.2017.11.064;
RA Anding A.L., Wang C., Chang T.K., Sliter D.A., Powers C.M., Hofmann K.,
RA Youle R.J., Baehrecke E.H.;
RT "Vps13D Encodes a Ubiquitin-Binding Protein that Is Required for the
RT Regulation of Mitochondrial Size and Clearance.";
RL Curr. Biol. 28:287-295(2018).
RN [16]
RP FUNCTION, INVOLVEMENT IN SCAR4, VARIANTS SCAR4 662-GLN--SER-4388 DEL;
RP 1106-GLN--SER-4388 DEL; ASP-1190; LEU-1307; 1803-TYR--SER-4388 DEL;
RP 2277-LEU--SER-4388 DEL; 2572-GLN--SER-4388 DEL; ILE-4107; SER-4149 AND
RP VAL-4210, AND CHARACTERIZATION OF VARIANTS SCAR4 1106-GLN--SER-4388 DEL;
RP ASP-1190; 1803-TYR--SER-4388 DEL AND VAL-4210.
RX PubMed=29604224; DOI=10.1002/ana.25220;
RA Seong E., Insolera R., Dulovic M., Kamsteeg E.J., Trinh J., Brueggemann N.,
RA Sandford E., Li S., Ozel A.B., Li J.Z., Jewett T., Kievit A.J.A.,
RA Muenchau A., Shakkottai V., Klein C., Collins C.A., Lohmann K.,
RA van de Warrenburg B.P., Burmeister M.;
RT "Mutations in VPS13D lead to a new recessive ataxia with spasticity and
RT mitochondrial defects.";
RL Ann. Neurol. 83:1075-1088(2018).
RN [17]
RP INVOLVEMENT IN SCAR4, AND VARIANTS SCAR4 ALA-865; ASP-1200; SER-2900;
RP GLN-3253; SER-3521 AND GLN-4228.
RX PubMed=29518281; DOI=10.1002/ana.25204;
RA Gauthier J., Meijer I.A., Lessel D., Mencacci N.E., Krainc D., Hempel M.,
RA Tsiakas K., Prokisch H., Rossignol E., Helm M.H., Rodan L.H.,
RA Karamchandani J., Carecchio M., Lubbe S.J., Telegrafi A., Henderson L.B.,
RA Lorenzo K., Wallace S.E., Glass I.A., Hamdan F.F., Michaud J.L.,
RA Rouleau G.A., Campeau P.M.;
RT "Recessive mutations in VPS13D cause childhood onset movement disorders.";
RL Ann. Neurol. 83:1089-1095(2018).
CC -!- FUNCTION: Mediates the transfer of lipids between membranes at
CC organelle contact sites (By similarity). Functions in promoting
CC mitochondrial clearance by mitochondrial autophagy (mitophagy), also
CC possibly by positively regulating mitochondrial fission
CC (PubMed:29307555, PubMed:29604224). Mitophagy plays an important role
CC in regulating cell health and mitochondrial size and homeostasis.
CC {ECO:0000250|UniProtKB:Q07878, ECO:0000269|PubMed:29307555,
CC ECO:0000269|PubMed:29604224}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1 {ECO:0000269|PubMed:15498460}; Synonyms=1A
CC {ECO:0000269|PubMed:15498460};
CC IsoId=Q5THJ4-1; Sequence=Displayed;
CC Name=2 {ECO:0000269|PubMed:15498460}; Synonyms=2A
CC {ECO:0000269|PubMed:15498460};
CC IsoId=Q5THJ4-2; Sequence=VSP_052249;
CC -!- TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:15498460}.
CC -!- DOMAIN: The UBA domain is required for mitochondrial size regulation.
CC {ECO:0000269|PubMed:29307555}.
CC -!- DISEASE: Spinocerebellar ataxia, autosomal recessive 4 (SCAR4)
CC [MIM:607317]: A form of spinocerebellar ataxia, a clinically and
CC genetically heterogeneous group of cerebellar disorders due to
CC degeneration of the cerebellum with variable involvement of the
CC brainstem and spinal cord. SCAR4 patients manifest ataxic gait with
CC spasticity and hyperreflexia of the lower limbs resulting in difficulty
CC walking. The age at onset is highly variable, ranging from early
CC childhood to adulthood. {ECO:0000269|PubMed:29518281,
CC ECO:0000269|PubMed:29604224}. Note=The disease is caused by variants
CC affecting the gene represented in this entry.
CC -!- SIMILARITY: Belongs to the VPS13 family. {ECO:0000255}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC86054.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAE46021.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AJ608774; CAE75586.1; -; mRNA.
DR EMBL; AJ608775; CAE75587.1; -; mRNA.
DR EMBL; BX784395; CAI19412.1; -; Genomic_DNA.
DR EMBL; AL031276; CAI19412.1; JOINED; Genomic_DNA.
DR EMBL; AL031296; CAI19412.1; JOINED; Genomic_DNA.
DR EMBL; AL109757; CAI19412.1; JOINED; Genomic_DNA.
DR EMBL; BX682532; CAI19412.1; JOINED; Genomic_DNA.
DR EMBL; BX784396; CAI19412.1; JOINED; Genomic_DNA.
DR EMBL; BX784396; CAI19414.1; -; Genomic_DNA.
DR EMBL; AL031276; CAI19414.1; JOINED; Genomic_DNA.
DR EMBL; AL031296; CAI19414.1; JOINED; Genomic_DNA.
DR EMBL; AL109757; CAI19414.1; JOINED; Genomic_DNA.
DR EMBL; BX682532; CAI19414.1; JOINED; Genomic_DNA.
DR EMBL; BX784395; CAI19414.1; JOINED; Genomic_DNA.
DR EMBL; AL162331; CAB82724.1; -; mRNA.
DR EMBL; AB007922; BAA32298.3; -; mRNA.
DR EMBL; AK125118; BAC86054.1; ALT_SEQ; mRNA.
DR EMBL; BX641035; CAE46021.1; ALT_FRAME; mRNA.
DR EMBL; BC028115; AAH28115.1; -; mRNA.
DR EMBL; BC051804; AAH51804.1; -; mRNA.
DR CCDS; CCDS30588.1; -. [Q5THJ4-1]
DR CCDS; CCDS30589.1; -. [Q5THJ4-2]
DR PIR; T00067; T00067.
DR RefSeq; NP_056193.2; NM_015378.3. [Q5THJ4-1]
DR RefSeq; NP_060626.2; NM_018156.3. [Q5THJ4-2]
DR BioGRID; 120485; 57.
DR IntAct; Q5THJ4; 15.
DR STRING; 9606.ENSP00000478104; -.
DR GlyGen; Q5THJ4; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; Q5THJ4; -.
DR PhosphoSitePlus; Q5THJ4; -.
DR BioMuta; VPS13D; -.
DR DMDM; 74756617; -.
DR EPD; Q5THJ4; -.
DR jPOST; Q5THJ4; -.
DR MassIVE; Q5THJ4; -.
DR MaxQB; Q5THJ4; -.
DR PaxDb; Q5THJ4; -.
DR PeptideAtlas; Q5THJ4; -.
DR PRIDE; Q5THJ4; -.
DR ProteomicsDB; 65151; -. [Q5THJ4-1]
DR ProteomicsDB; 65152; -. [Q5THJ4-2]
DR Antibodypedia; 63052; 35 antibodies from 9 providers.
DR DNASU; 55187; -.
DR Ensembl; ENST00000613099.4; ENSP00000482233.1; ENSG00000048707.15. [Q5THJ4-2]
DR Ensembl; ENST00000620676.6; ENSP00000478104.1; ENSG00000048707.15. [Q5THJ4-1]
DR GeneID; 55187; -.
DR KEGG; hsa:55187; -.
DR MANE-Select; ENST00000620676.6; ENSP00000478104.1; NM_015378.4; NP_056193.2.
DR UCSC; uc031tou.2; human. [Q5THJ4-1]
DR CTD; 55187; -.
DR DisGeNET; 55187; -.
DR GeneCards; VPS13D; -.
DR GeneReviews; VPS13D; -.
DR HGNC; HGNC:23595; VPS13D.
DR HPA; ENSG00000048707; Low tissue specificity.
DR MalaCards; VPS13D; -.
DR MIM; 607317; phenotype.
DR MIM; 608877; gene.
DR neXtProt; NX_Q5THJ4; -.
DR OpenTargets; ENSG00000048707; -.
DR Orphanet; 95434; Autosomal recessive cerebellar ataxia-movement disorder syndrome.
DR PharmGKB; PA134970144; -.
DR VEuPathDB; HostDB:ENSG00000048707; -.
DR eggNOG; KOG1796; Eukaryota.
DR eggNOG; KOG1809; Eukaryota.
DR GeneTree; ENSGT00950000183083; -.
DR InParanoid; Q5THJ4; -.
DR OMA; LFGTCPT; -.
DR OrthoDB; 4159at2759; -.
DR PhylomeDB; Q5THJ4; -.
DR TreeFam; TF300316; -.
DR PathwayCommons; Q5THJ4; -.
DR SignaLink; Q5THJ4; -.
DR BioGRID-ORCS; 55187; 556 hits in 1083 CRISPR screens.
DR ChiTaRS; VPS13D; human.
DR GeneWiki; VPS13D; -.
DR GenomeRNAi; 55187; -.
DR Pharos; Q5THJ4; Tdark.
DR PRO; PR:Q5THJ4; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; Q5THJ4; protein.
DR Bgee; ENSG00000048707; Expressed in skin of leg and 202 other tissues.
DR ExpressionAtlas; Q5THJ4; baseline and differential.
DR Genevisible; Q5THJ4; HS.
DR GO; GO:0070062; C:extracellular exosome; HDA:UniProtKB.
DR GO; GO:0019898; C:extrinsic component of membrane; IBA:GO_Central.
DR GO; GO:0006869; P:lipid transport; IEA:UniProtKB-KW.
DR GO; GO:0007005; P:mitochondrion organization; IMP:UniProtKB.
DR GO; GO:1901526; P:positive regulation of mitophagy; IMP:UniProtKB.
DR GO; GO:0045053; P:protein retention in Golgi apparatus; IBA:GO_Central.
DR GO; GO:0006623; P:protein targeting to vacuole; IBA:GO_Central.
DR CDD; cd14306; UBA_VP13D; 1.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR InterPro; IPR041969; VP13D_UBA.
DR InterPro; IPR026847; VPS13.
DR InterPro; IPR026854; VPS13-like_N.
DR InterPro; IPR031645; VPS13_C.
DR InterPro; IPR031642; VPS13_mid_rpt.
DR InterPro; IPR031646; VPS13_N2.
DR InterPro; IPR009543; VPS13_VAB.
DR PANTHER; PTHR16166; PTHR16166; 1.
DR Pfam; PF12624; Chorein_N; 1.
DR Pfam; PF06650; SHR-BD; 1.
DR Pfam; PF00627; UBA; 1.
DR Pfam; PF16908; VPS13; 1.
DR Pfam; PF16909; VPS13_C; 1.
DR Pfam; PF16910; VPS13_mid_rpt; 2.
DR SMART; SM00165; UBA; 1.
DR SUPFAM; SSF46934; SSF46934; 1.
DR PROSITE; PS50030; UBA; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Disease variant; Lipid transport;
KW Neurodegeneration; Phosphoprotein; Reference proteome; Transport.
FT CHAIN 1..4388
FT /note="Intermembrane lipid transfer protein VPS13D"
FT /id="PRO_0000262951"
FT DOMAIN 2..115
FT /note="Chorein N-terminal"
FT /evidence="ECO:0000255"
FT DOMAIN 2633..2676
FT /note="UBA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 3276..3558
FT /note="SHR-BD"
FT /evidence="ECO:0000255"
FT REGION 745..796
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1563..1582
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1741..1771
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2070..2108
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2122..2145
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 747..766
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 2070..2088
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 663
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163,
FT ECO:0007744|PubMed:24275569"
FT MOD_RES 1034
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 1038
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 1042
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:20068231,
FT ECO:0007744|PubMed:23186163"
FT MOD_RES 1138
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163,
FT ECO:0007744|PubMed:24275569"
FT MOD_RES 1341
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:24275569"
FT MOD_RES 1598
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 1603
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 1699
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 1761
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18669648,
FT ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163,
FT ECO:0007744|PubMed:24275569"
FT MOD_RES 1765
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:24275569"
FT MOD_RES 2435
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19690332,
FT ECO:0007744|PubMed:21406692"
FT MOD_RES 2671
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163,
FT ECO:0007744|PubMed:24275569"
FT MOD_RES 2861
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 2864
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 2983
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 3524
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT VAR_SEQ 2851..2876
FT /note="SLPLVYLRTRSTASLTNLEHQIYARA -> T (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039,
FT ECO:0000303|PubMed:15498460, ECO:0000303|PubMed:17974005"
FT /id="VSP_052249"
FT VARIANT 225
FT /note="A -> T (in dbSNP:rs12057307)"
FT /id="VAR_029557"
FT VARIANT 662..4388
FT /note="Missing (in SCAR4)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081496"
FT VARIANT 865
FT /note="T -> A (in SCAR4; dbSNP:rs1383958401)"
FT /evidence="ECO:0000269|PubMed:29518281"
FT /id="VAR_080911"
FT VARIANT 1106..4388
FT /note="Missing (in SCAR4; altered mitochondrial morphology
FT in patient cells)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081497"
FT VARIANT 1190
FT /note="G -> D (in SCAR4; altered mitochondrial morphology
FT in patient cells; dbSNP:rs1557680919)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081498"
FT VARIANT 1200
FT /note="G -> D (in SCAR4; dbSNP:rs768331333)"
FT /evidence="ECO:0000269|PubMed:29518281"
FT /id="VAR_080912"
FT VARIANT 1307
FT /note="M -> L (in SCAR4; unknown pathological significance;
FT dbSNP:rs775845475)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081499"
FT VARIANT 1341
FT /note="S -> L (in dbSNP:rs12407578)"
FT /id="VAR_029558"
FT VARIANT 1505
FT /note="E -> V (in dbSNP:rs4845898)"
FT /id="VAR_029559"
FT VARIANT 1624
FT /note="I -> T (in dbSNP:rs41279454)"
FT /id="VAR_062169"
FT VARIANT 1707
FT /note="S -> F (in dbSNP:rs958068)"
FT /id="VAR_029560"
FT VARIANT 1803..4388
FT /note="Missing (in SCAR4; decreased protein abundance;
FT altered mitochondrial morphology in patient cells)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081500"
FT VARIANT 2277..4388
FT /note="Missing (in SCAR4)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081501"
FT VARIANT 2572..4388
FT /note="Missing (in SCAR4)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081502"
FT VARIANT 2900
FT /note="L -> S (in SCAR4)"
FT /evidence="ECO:0000269|PubMed:29518281"
FT /id="VAR_080913"
FT VARIANT 3253
FT /note="R -> Q (in SCAR4; dbSNP:rs1191625571)"
FT /evidence="ECO:0000269|PubMed:29518281"
FT /id="VAR_080914"
FT VARIANT 3521
FT /note="N -> S (in SCAR4; dbSNP:rs1557737087)"
FT /evidence="ECO:0000269|PubMed:29518281"
FT /id="VAR_080915"
FT VARIANT 4107
FT /note="N -> I (in SCAR4; unknown pathological
FT significance)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081503"
FT VARIANT 4149
FT /note="G -> S (in SCAR4; unknown pathological
FT significance)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081504"
FT VARIANT 4210
FT /note="A -> V (in SCAR4; altered mitochondrial morphology
FT in patient cells; dbSNP:rs746736545)"
FT /evidence="ECO:0000269|PubMed:29604224"
FT /id="VAR_081505"
FT VARIANT 4228
FT /note="R -> Q (in SCAR4; dbSNP:rs1557478316)"
FT /evidence="ECO:0000269|PubMed:29518281"
FT /id="VAR_080916"
FT CONFLICT 2332
FT /note="I -> V (in Ref. 6; CAE46021)"
FT /evidence="ECO:0000305"
FT CONFLICT 2361
FT /note="C -> R (in Ref. 6; CAE46021)"
FT /evidence="ECO:0000305"
FT CONFLICT 2783
FT /note="S -> G (in Ref. 1; CAE75586/CAE75587)"
FT /evidence="ECO:0000305"
FT CONFLICT 2876
FT /note="Missing (in Ref. 6; BAA32298)"
FT /evidence="ECO:0000305"
FT CONFLICT 3203
FT /note="I -> T (in Ref. 7; AAH28115)"
FT /evidence="ECO:0000305"
FT CONFLICT 3332
FT /note="N -> S (in Ref. 6; CAE46021)"
FT /evidence="ECO:0000305"
FT CONFLICT 3379
FT /note="N -> S (in Ref. 6; CAE46021)"
FT /evidence="ECO:0000305"
FT CONFLICT 3400
FT /note="A -> T (in Ref. 6; CAE46021)"
FT /evidence="ECO:0000305"
FT CONFLICT 3678
FT /note="G -> E (in Ref. 6; CAE46021)"
FT /evidence="ECO:0000305"
FT CONFLICT 3994
FT /note="Q -> R (in Ref. 6; CAE46021)"
FT /evidence="ECO:0000305"
FT CONFLICT 4268
FT /note="A -> T (in Ref. 6; CAE46021)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 4388 AA; 491916 MW; 799681E3BE2D1DDD CRC64;
MLEGLVAWVL NTYLGKYVNN LNTDQLSVAL LKGAVELENL PLKKDALKEL ELPFEVKAGF
IGKVTLQIPF YRPHVDPWVI SISSLHLIGA PEKIQDFNDE KEKLLERERK KALLQALEEK
WKNDRQQKGE SYWYSVTASV VTRIVENIEL KIQDVHLRFE DGVTNPSHPF AFGICIKNVS
MQNAVNEPVQ KLMRKKQLDV AEFSIYWDVD CTLLGDLPQM ELQEAMARSM ESRSHHYVLE
PVFASALLKR NCSKKPLRSR HSPRIDCDIQ LETIPLKLSQ LQYRQIMEFL KELERKERQV
KFRRWKPKVA ISKNCREWWY FALNANLYEI REQRKRCTWD FMLHRARDAV SYTDKYFNKL
KGGLLSTDDK EEMCRIEEEQ SFEELKILRE LVHDRFHKQE ELAESLREPQ FDSPGACPGA
PEPGGGSGML QYLQSWFPGW GGWYGQQTPE GNVVEGLSAE QQEQWIPEEI LGTEEFFDPT
ADASCMNTYT KRDHVFAKLN LQLQRGTVTL LHKEQGTPQM NESAFMQLEF SDVKLLAESL
PRRNSSLLSV RLGGLFLRDL ATEGTMFPLL VFPNPQKEVG RVSQSFGLQT TSADRSDHYP
AADPDGPVFE MLYERNPAHS HFERRLNVST RPLNIIYNPQ AIKKVADFFY KGKVHTSGFG
YQSELELRVA EAARRQYNKL KMQTKAEIRQ TLDRLLVGDF IEESKRWTVR LDISAPQVIF
PDDFKFKNPV LVVVDLGRML LTNTQDNSRR KSRDGSASEE TQFSDDEYKT PLATPPNTPP
PESSSSNGEK TPPFSGVEFS EEQLQAHLMS TKMYERYSLS FMDLQIMVGR VKDNWKHVQD
IDVGPTHVVE KFNVHLQLER RLIYTSDPKY PGAVLSGNLP DLKIHINEDK ISALKNCFAL
LTTPEMKTSD TQIKEKIFPQ EEQRGSLQDS VMNLTQSIVL LEQHTREVLV ESQLLLAEFK
VNCMQLGVES NGRYISVLKV FGTNAHFVKR PYDAEVSLTV HGLLLVDTMQ TYGADFDLLM
ASHKNLSFDI PTGSLRDSRA QSPVSGPNVA HLTDGATLND RSATSVSLDK ILTKEQESLI
KLEYQFVSSE CPSMNLDSTL QVISLQVNNL DIILNPETIV ELIGFLQKSF PKEKDDLSPQ
PLMTDFERSF REQGTYQSTY EQNTEVAVEI HRLNLLLLRT VGMANREKYG RKIATASIGG
TKVNVSMGST FDMNGSLGCL QLMDLTQDNV KNQYVVSIGN SVGYENIISD IGYFESVFVR
MEDAALTEAL SFTFVERSKQ ECFLNLKMAS LHYNHSAKFL KELTLSMDEL EENFRGMLKS
AATKVTTVLA TKTAEYSEMV SLFETPRKTR EPFILEENEI YGFDLASSHL DTVKLILNIN
IESPVVSIPR KPGSPELLVG HLGQIFIQNF VAGDDESRSD RLQVEIKDIK LYSLNCTQLA
GREAVGSEGS RMFCPPSGSG SANSQEEAHF TRHDFFESLH RGQAFHILNN TTIQFKLEKI
PIERESELTF SLSPDDLGTS SIMKIEGKFV NPVQVVLAKH VYEQVLQTLD NLVYSEDLNK
YPASATSSPC PDSPLPPLST CGESSVERKE NGLFSHSSLS NTSQKSLSVK EVKSFTQIQA
TFCISELQVQ LSGDLTLGAQ GLVSLKFQDF EVEFSKDHPQ TLSIQIALHS LLMEDLLEKN
PDSKYKNLMV SRGAPKPSSL AQKEYLSQSC PSVSNVEYPD MPRSLPSHME EAPNVFQLYQ
RPTSASRKKQ KEVQDKDYPL TPPPSPTVDE PKILVGKSKF DDSLVHINIF LVDKKHPEFS
SSYNRVNRSI DVDFNCLDVL ITLQTWVVIL DFFGIGSTAD NHAMRLPPEG ILHNVKLEPH
ASMESGLQDP VNTKLDLKVH SLSLVLNKTT SELAKANVSK LVAHLEMIEG DLALQGSIGS
LSLSDLTCHG EFYRERFTTS GEEALIFQTF KYGRPDPLLR REHDIRVSLR MASVQYVHTQ
RFQAEVVAFI QHFTQLQDVL GRQRAAIEGQ TVRDQAQRCS RVLLDIEAGA PVLLIPESSR
SNNLIVANLG KLKVKNKFLF AGFPGTFSLQ DKESVPSASP TGIPKHSLRK TTSTEEPRGT
HSQGQFTMPL AGMSLGSLKS EFVPSTSTKQ QGPQPTLSVG QESSSPEDHV CLLDCVVVDL
QDMDIFAAER HPREYSKAPE DSSGDLIFPS YFVRQTGGSL LTEPCRLKLQ VERNLDKEIS
HTVPDISIHG NLSSVHCSLD LYKYKLIRGL LENNLGEPIE EFMRPYDLQD PRIHTVLSGE
VYTCMCFLID MVNVSLELKD PKRKEGAGSL ARFDFKKCKL LYESFSNQTK SINLVSHSMM
AFDTRYAGQK TSPGMTNVFS CIFQPAKNSS TTQGSIQIEL HFRSTKDSSC FTVVLNNLRV
FLIFDWLLLV HDFLHTPSDI KKQNHVTPSR HRNSSSESAI VPKTVKSGVV TKRSSLPVSN
ERHLEVKVNV TGTEFVVIED VSCFDTNAII LKGTTVLTYK PRFVDRPFSG SLFGIEVFSC
RLGNEHDTAL SIVDPVQIQM ELVGNSSYQN SSGLMDAFNS EDFPPVLEIQ LQALDIRLSY
NDVQLFLAIA KSIPEQANAA VPDSVALESD SVGTYLPGAS RVGEEIREGT RHTLDPVLEL
QLARLQELGF SMDDCRKALL ACQGQLKKAA SWLFKNAEPL KSLSLASTSR DSPGAVAAPL
ISGVEIKAES VCICFIDDCM DCDVPLAELT FSRLNFLQRV RTSPEGYAHF TLSGDYYNRA
LSGWEPFIEP WPCSVSWQQQ AASRLHPPRL KLEAKAKPRL DINITSVLID QYVSTKESWM
ADYCKDDKDI ESAKSEDWMG SSVDPPCFGQ SLPLVYLRTR STASLTNLEH QIYARAEVKT
PKRRQPFVPF ALRNHTGCTL WFATLTTTPT RAALSHSGSP GVVPEGNGTF LDDTHNVSEW
REVLTGEEIP FEFEARGKLR HRHTHDLRIH QLQVRVNGWE QVSPVSVDKV GTFFRYAAPD
KNSSSSTIGS PSSRTNIIHP QVYFSSLPPV RVVFAVTMEG SARKVITVRS ALIVRNRLET
PMELRLDSPS APDKPVVLPA IMPGDSFAVP LHLTSWRLQA RPKGLGVFFC KAPIHWTNVV
KTAEISSSKR ECHSMDTEKS RFFRFCVAIK KENYPDYMPS NIFSDSAKQI FRQPGHTIYL
LPTVVICNLL PCELDFYVKG MPINGTLKPG KEAALHTADT SQNIELGVSL ENFPLCKELL
IPPGTQNYMV RMRLYDVNRR QLNLTIRIVC RAEGSLKIFI SAPYWLINKT GLPLIFRQDN
AKTDAAGQFE EHELARSLSP LLFCYADKEQ PNLCTMRIGR GIHPEGMPGW CQGFSLDGGS
GVRALKVIQQ GNRPGLIYNI GIDVKKGRGR YIDTCMVIFA PRYLLDNKSS HKLAFAQREF
ARGQGTANPE GYISTLPGSS VVFHWPRNDY DQLLCVRLMD VPNCIWSGGF EVNKNNSFHI
NMRDTLGKCF FLRVEITLRG ATYRISFSDT DQLPPPFRID NFSKVPVVFT QHGVAEPRLR
TEVKPMTSLD YAWDEPTLPP FITLTVKGAG SSEINCNMND FQDNRQLYYE NFIYIAATYT
FSGLQEGTGR PVASNKAITC AELVLDVSPK TQRVILKKKE PGKRSQLWRM TGTGMLAHEG
SSVPHNPNKP SAARSTEGSA ILDIAGLAAV TDNRYEPLML RKPDRRRSTT QTWSFREGKL
TCGLHGLVVQ AKGGLSGLFD GAEVVLGPDT SMELLGPVPP EQQFINQKMR PGSGMLSIRV
IPDGPTRALQ ITDFCHRKSS RSYEVDELPV TEQELQKLKN PDTEQELEVL VRLEGGIGLS
LINKVPEELV FASLTGINVH YTQLATSHML ELSIQDVQVD NQLIGTTQPF MLYVTPLSNE
NEVIETGPAV QVNAVKFPSK SALTNIYKHL MITAQRFTVQ IEEKLLLKLL SFFGYDQAES
EVEKYDENLH EKTAEQGGTP IRYYFENLKI SIPQIKLSVF TSNKLPLDLK ALKSTLGFPL
IRFEDAVINL DPFTRVHPYE TKEFIINDIL KHFQEELLSQ AARILGSVDF LGNPMGLLND
VSEGVTGLIK YGNVGGLIRN VTHGVSNSAA KFAGTLSDGL GKTMDNRHQS EREYIRYHAA
TSGEHLVAGI HGLAHGIIGG LTSVITSTVE GVKTEGGVSG FISGLGKGLV GTVTKPVAGA
LDFASETAQA VRDTATLSGP RTQAQRVRKP RCCTGPQGLL PRYSESQAEG QEQLFKLTDN
IQDEFFIAVE NIDSYCVLIS SKAVYFLKSG DYVDREAIFL EVKYDDLYHC LVSKDHGKVY
VQVTKKAVST SSGVSIPGPS HQKPMVHVKS EVLAVKLSQE INYAKSLYYE QQLMLRLSEN
REQLELDS
