DYM_HUMAN
ID DYM_HUMAN Reviewed; 669 AA.
AC Q7RTS9; A8K5I8; B2RCF9; B4DKI7; Q3ZTS8; Q6P2P5; Q8N2M0; Q9BVE9; Q9NPU7;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-2003, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Dymeclin;
DE AltName: Full=Dyggve-Melchior-Clausen syndrome protein;
GN Name=DYM;
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]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], INVOLVEMENT IN DMC, AND TISSUE
RP SPECIFICITY.
RX PubMed=12554689; DOI=10.1093/hmg/ddg029;
RA El Ghouzzi V., Dagoneau N., Kinning E., Thauvin-Robinet C., Chemaitilly W.,
RA Prost-Squarcioni C., Al-Gazali L.I., Verloes A., Le Merrer M., Munnich A.,
RA Trembath R.C., Cormier-Daire V.;
RT "Mutations in a novel gene dymeclin (FLJ20071) are responsible for Dyggve-
RT Melchior-Clausen syndrome.";
RL Hum. Mol. Genet. 12:357-364(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Cervix, Testis, and Tongue;
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Brain, and Cervix;
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 [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-524 (ISOFORM 1).
RA Kemmer D., Podowski R., Hodges E., Roth P., Lenhard B., Sonnhammer E.L.L.,
RA Wasserman W.W., Hoog C.;
RT "Characterization of human proteins containing evolutionary conserved
RT domains of unknown function.";
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 446-669.
RC TISSUE=Melanoma;
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]
RP TISSUE SPECIFICITY, SUBCELLULAR LOCATION, MYRISTOYLATION AT GLY-2,
RP MUTAGENESIS OF GLY-2, CHARACTERIZATION OF VARIANT SMC1 LYS-87, AND
RP CHARACTERIZATION OF VARIANT DMC TYR-469.
RX PubMed=18996921; DOI=10.1093/hmg/ddn371;
RA Dimitrov A., Paupe V., Gueudry C., Sibarita J.-B., Raposo G.,
RA Vielemeyer O., Gilbert T., Csaba Z., Attie-Bitach T., Cormier-Daire V.,
RA Gressens P., Rustin P., Perez F., El Ghouzzi V.;
RT "The gene responsible for Dyggve-Melchior-Clausen syndrome encodes a novel
RT peripheral membrane protein dynamically associated with the Golgi
RT apparatus.";
RL Hum. Mol. Genet. 18:440-453(2009).
RN [8]
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH GOLM1 AND PPIB, AND
RP INVOLVEMENT IN DCM.
RX PubMed=21280149; DOI=10.1002/humu.21413;
RA Denais C., Dent C.L., Southgate L., Hoyle J., Dafou D., Trembath R.C.,
RA Machado R.D.;
RT "Dymeclin, the gene underlying Dyggve-Melchior-Clausen syndrome, encodes a
RT protein integral to extracellular matrix and Golgi organization and is
RT associated with protein secretion pathways critical in bone development.";
RL Hum. Mutat. 32:231-239(2011).
RN [9]
RP MYRISTOYLATION AT GLY-2, CLEAVAGE OF INITIATOR METHIONINE, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=25255805; DOI=10.1038/ncomms5919;
RA Thinon E., Serwa R.A., Broncel M., Brannigan J.A., Brassat U., Wright M.H.,
RA Heal W.P., Wilkinson A.J., Mann D.J., Tate E.W.;
RT "Global profiling of co- and post-translationally N-myristoylated proteomes
RT in human cells.";
RL Nat. Commun. 5:4919-4919(2014).
RN [10]
RP VARIANT DMC TYR-469, AND VARIANT SMC1 LYS-87.
RX PubMed=12491225; DOI=10.1086/346176;
RA Cohn D.H., Ehtesham N., Krakow D., Unger S., Shanske A., Reinker K.,
RA Powell B.R., Rimoin D.L.;
RT "Mental retardation and abnormal skeletal development (Dyggve-Melchior-
RT Clausen dysplasia) due to mutations in a novel, evolutionarily conserved
RT gene.";
RL Am. J. Hum. Genet. 72:419-428(2003).
RN [11]
RP VARIANT SMC1 ARG-542.
RX PubMed=19005420; DOI=10.1097/mcd.0b013e32831868ea;
RA Santos H.G., Fernandes H.C., Nunes J.L., Almeida M.R.;
RT "Portuguese case of Smith-McCort syndrome caused by a new mutation in the
RT dymeclin (FLJ20071) gene.";
RL Clin. Dysmorphol. 18:41-44(2009).
CC -!- FUNCTION: Necessary for correct organization of Golgi apparatus.
CC Involved in bone development. {ECO:0000269|PubMed:21280149}.
CC -!- SUBUNIT: Interacts with GOLM1 and PPIB. {ECO:0000269|PubMed:21280149}.
CC -!- INTERACTION:
CC Q7RTS9; Q8NBJ4: GOLM1; NbExp=3; IntAct=EBI-2871106, EBI-712073;
CC Q7RTS9; P23284: PPIB; NbExp=4; IntAct=EBI-2871106, EBI-359252;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Golgi apparatus. Membrane
CC {ECO:0000305}; Lipid-anchor {ECO:0000305}. Note=Sequence analysis
CC programs clearly predict 1 transmembrane region. However,
CC PubMed:18996921 shows that it is not a stably anchored transmembrane
CC protein but it weakly associates with the Golgi apparatus and shuttles
CC between the Golgi and the cytosol.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q7RTS9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q7RTS9-2; Sequence=VSP_036442, VSP_036443;
CC -!- TISSUE SPECIFICITY: Expressed in most embryo-fetal and adult tissues.
CC Abundant in primary chondrocytes, osteoblasts, cerebellum, kidney,
CC lung, stomach, heart, pancreas and fetal brain. Very low or no
CC expression in the spleen, thymus, esophagus, bladder and thyroid gland.
CC {ECO:0000269|PubMed:12554689, ECO:0000269|PubMed:18996921}.
CC -!- PTM: Myristoylated in vitro; myristoylation is not essential for
CC protein targeting to Golgi compartment. {ECO:0000269|PubMed:18996921}.
CC -!- DISEASE: Dyggve-Melchior-Clausen syndrome (DMC) [MIM:223800]: A rare
CC autosomal recessive disorder belonging to the group of
CC spondyloepimetaphyseal dysplasias. DMC is characterized by progressive
CC short stature with short trunk dwarfism, microcephaly, protruding
CC sternum, and psychomotor retardation. Radiological features include a
CC platyspondyly with double vertebral humps, an epiphyso-metaphyseal
CC dysplasia and lacy pelvis iliac crests. {ECO:0000269|PubMed:12491225,
CC ECO:0000269|PubMed:12554689, ECO:0000269|PubMed:18996921}. Note=The
CC disease is caused by variants affecting the gene represented in this
CC entry.
CC -!- DISEASE: Smith-McCort dysplasia 1 (SMC1) [MIM:607326]: A rare autosomal
CC recessive osteochondrodysplasia with skeletal features identical to
CC those of Dyggve-Melchior-Clausen syndrome, but with normal intelligence
CC and no microcephaly. It is characterized by short limbs and trunk with
CC barrel-shaped chest. The radiographic phenotype includes platyspondyly,
CC generalized abnormalities of the epiphyses and metaphyses, and a
CC distinctive lacy appearance of the iliac crest.
CC {ECO:0000269|PubMed:12491225, ECO:0000269|PubMed:18996921,
CC ECO:0000269|PubMed:19005420}. Note=The disease is caused by variants
CC affecting the gene represented in this entry.
CC -!- SIMILARITY: Belongs to the dymeclin family. {ECO:0000305}.
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DR EMBL; BK000950; DAA00396.1; -; Genomic_DNA.
DR EMBL; AK074611; BAC11088.1; -; mRNA.
DR EMBL; AK091256; BAG52319.1; -; mRNA.
DR EMBL; AK291303; BAF83992.1; -; mRNA.
DR EMBL; AK296579; BAG59199.1; -; mRNA.
DR EMBL; AK315091; BAG37556.1; -; mRNA.
DR EMBL; CH471096; EAW62933.1; -; Genomic_DNA.
DR EMBL; BC001252; AAH01252.2; -; mRNA.
DR EMBL; BC064394; AAH64394.1; -; mRNA.
DR EMBL; AY364250; AAQ76809.1; -; mRNA.
DR EMBL; AL390156; CAB99092.1; -; mRNA.
DR CCDS; CCDS11937.1; -. [Q7RTS9-1]
DR RefSeq; NP_060123.3; NM_017653.3. [Q7RTS9-1]
DR AlphaFoldDB; Q7RTS9; -.
DR BioGRID; 120165; 165.
DR ELM; Q7RTS9; -.
DR IntAct; Q7RTS9; 21.
DR STRING; 9606.ENSP00000269445; -.
DR GlyGen; Q7RTS9; 2 sites, 1 O-linked glycan (2 sites).
DR iPTMnet; Q7RTS9; -.
DR PhosphoSitePlus; Q7RTS9; -.
DR BioMuta; DYM; -.
DR DMDM; 68565365; -.
DR EPD; Q7RTS9; -.
DR jPOST; Q7RTS9; -.
DR MassIVE; Q7RTS9; -.
DR MaxQB; Q7RTS9; -.
DR PaxDb; Q7RTS9; -.
DR PeptideAtlas; Q7RTS9; -.
DR PRIDE; Q7RTS9; -.
DR ProteomicsDB; 68896; -. [Q7RTS9-1]
DR ProteomicsDB; 68897; -. [Q7RTS9-2]
DR Antibodypedia; 22572; 134 antibodies from 22 providers.
DR DNASU; 54808; -.
DR Ensembl; ENST00000269445.10; ENSP00000269445.6; ENSG00000141627.14. [Q7RTS9-1]
DR Ensembl; ENST00000442713.6; ENSP00000395942.2; ENSG00000141627.14. [Q7RTS9-2]
DR GeneID; 54808; -.
DR KEGG; hsa:54808; -.
DR UCSC; uc002ldi.2; human. [Q7RTS9-1]
DR CTD; 54808; -.
DR DisGeNET; 54808; -.
DR GeneCards; DYM; -.
DR HGNC; HGNC:21317; DYM.
DR HPA; ENSG00000141627; Low tissue specificity.
DR MalaCards; DYM; -.
DR MIM; 223800; phenotype.
DR MIM; 607326; phenotype.
DR MIM; 607461; gene.
DR neXtProt; NX_Q7RTS9; -.
DR OpenTargets; ENSG00000141627; -.
DR Orphanet; 239; Dyggve-Melchior-Clausen disease.
DR Orphanet; 178355; Smith-McCort dysplasia.
DR PharmGKB; PA134879547; -.
DR VEuPathDB; HostDB:ENSG00000141627; -.
DR eggNOG; KOG2225; Eukaryota.
DR GeneTree; ENSGT00390000008772; -.
DR HOGENOM; CLU_013309_2_0_1; -.
DR InParanoid; Q7RTS9; -.
DR OrthoDB; 982213at2759; -.
DR PhylomeDB; Q7RTS9; -.
DR TreeFam; TF314870; -.
DR PathwayCommons; Q7RTS9; -.
DR SignaLink; Q7RTS9; -.
DR BioGRID-ORCS; 54808; 15 hits in 1086 CRISPR screens.
DR ChiTaRS; DYM; human.
DR GeneWiki; DYM; -.
DR GenomeRNAi; 54808; -.
DR Pharos; Q7RTS9; Tbio.
DR PRO; PR:Q7RTS9; -.
DR Proteomes; UP000005640; Chromosome 18.
DR RNAct; Q7RTS9; protein.
DR Bgee; ENSG00000141627; Expressed in bone marrow cell and 178 other tissues.
DR ExpressionAtlas; Q7RTS9; baseline and differential.
DR Genevisible; Q7RTS9; HS.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005794; C:Golgi apparatus; IDA:UniProtKB.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0019899; F:enzyme binding; IPI:UniProtKB.
DR GO; GO:0060348; P:bone development; IMP:UniProtKB.
DR GO; GO:0007030; P:Golgi organization; IMP:UniProtKB.
DR InterPro; IPR019142; Dymeclin.
DR PANTHER; PTHR12895; PTHR12895; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; Disease variant; Dwarfism;
KW Golgi apparatus; Lipoprotein; Membrane; Myristate; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:25255805"
FT CHAIN 2..669
FT /note="Dymeclin"
FT /id="PRO_0000086883"
FT LIPID 2
FT /note="N-myristoyl glycine"
FT /evidence="ECO:0000269|PubMed:25255805,
FT ECO:0000305|PubMed:18996921"
FT VAR_SEQ 65
FT /note="V -> A (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_036442"
FT VAR_SEQ 66..255
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_036443"
FT VARIANT 87
FT /note="E -> K (in SMC1; does not affect protein
FT localization; dbSNP:rs120074164)"
FT /evidence="ECO:0000269|PubMed:12491225,
FT ECO:0000269|PubMed:18996921"
FT /id="VAR_022740"
FT VARIANT 469
FT /note="N -> Y (in DMC; results in protein mis-localization
FT and aggregation; dbSNP:rs120074163)"
FT /evidence="ECO:0000269|PubMed:12491225,
FT ECO:0000269|PubMed:18996921"
FT /id="VAR_054499"
FT VARIANT 542
FT /note="C -> R (in SMC1; dbSNP:rs120074165)"
FT /evidence="ECO:0000269|PubMed:19005420"
FT /id="VAR_065293"
FT MUTAGEN 2
FT /note="G->A: Does not affect protein localization to Golgi
FT apparatus. Prevents myristoylation in vitro."
FT /evidence="ECO:0000269|PubMed:18996921"
FT CONFLICT 66
FT /note="E -> K (in Ref. 2; BAC11088)"
FT /evidence="ECO:0000305"
FT CONFLICT 249
FT /note="L -> P (in Ref. 2; BAC11088)"
FT /evidence="ECO:0000305"
FT CONFLICT 381
FT /note="E -> G (in Ref. 3; BAF83992)"
FT /evidence="ECO:0000305"
FT CONFLICT 408
FT /note="D -> Y (in Ref. 4; AAH64394)"
FT /evidence="ECO:0000305"
FT CONFLICT 453
FT /note="R -> K (in Ref. 3; BAF83992)"
FT /evidence="ECO:0000305"
FT CONFLICT 537
FT /note="E -> G (in Ref. 3; BAF83992)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 669 AA; 75935 MW; 7C8A216A09DBE43F CRC64;
MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLVENNPR TGNLGALIKV FLSRTKELKL SAECQNHIFI WQTHNALFII CCLLKVFICQ
MSEEELQLHF TYEEKSPGNY SSDSEDLLEE LLCCLMQLIT DIPLLDITYE ISVEAISTMV
VFLSCQLFHK EVLRQSISHK YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS
DGGGLLYGLA SGVATGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA
PNPYRQAIMS FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS
NIRTYMLART DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK
NITWYSERVL TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY
AAQRIISLFS LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN
SCLTNSLHHN PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV
ERVLEIIKQG VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD
IQLFTMDSD
