PTHD3_HUMAN
ID PTHD3_HUMAN Reviewed; 954 AA.
AC Q3KNS1; F6LPT1; I3L499; Q6ZU28;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 25-MAY-2022, sequence version 4.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Patched domain-containing protein 3;
DE AltName: Full=Patched-related protein;
GN Name=PTCHD3; Synonyms=PTR;
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:0000312|EMBL:AEA72435.1}
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, SUBCELLULAR LOCATION,
RP TISSUE SPECIFICITY, POLYMORPHISM, AND VARIANT GLY-473.
RC TISSUE=Lymph node {ECO:0000312|EMBL:AEA72435.1};
RX PubMed=21439084; DOI=10.1186/1471-2350-12-45;
RA Ghahramani Seno M.M., Kwan B.Y., Lee-Ng K.K., Moessner R., Lionel A.C.,
RA Marshall C.R., Scherer S.W.;
RT "Human PTCHD3 nulls: rare copy number and sequence variants suggest a non-
RT essential gene.";
RL BMC Med. Genet. 12:45-45(2011).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15164054; DOI=10.1038/nature02462;
RA Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L.,
RA Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K.,
RA Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L.,
RA Taylor A., Battles J., Bird C.P., Ainscough R., Almeida J.P.,
RA Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J.,
RA Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y.,
RA Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P.,
RA Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N.,
RA Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A.,
RA Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C.,
RA Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D.,
RA Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C.,
RA Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K.,
RA Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A.,
RA Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S.,
RA McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S.,
RA Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V.,
RA Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A.,
RA Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M.,
RA Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A.,
RA Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P.,
RA Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y.,
RA Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D.,
RA Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.;
RT "The DNA sequence and comparative analysis of human chromosome 10.";
RL Nature 429:375-381(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-804, AND VARIANTS GLY-473;
RP THR-521 AND MET-584.
RC TISSUE=Testis;
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-767, AND VARIANTS PRO-152 AND
RP MET-584.
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 FUNCTION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=17904097; DOI=10.1016/j.bbrc.2007.09.047;
RA Fan J., Akabane H., Zheng X., Zhou X., Zhang L., Liu Q., Zhang Y.-L.,
RA Yang J., Zhu G.-Z.;
RT "Male germ cell-specific expression of a novel patched-domain containing
RT gene Ptchd3.";
RL Biochem. Biophys. Res. Commun. 363:757-761(2007).
CC -!- FUNCTION: May play a role in sperm development or sperm function
CC (PubMed:17904097). However, does not appear to have an essential role
CC in spermatogenesis or male fertility (PubMed:21439084).
CC {ECO:0000269|PubMed:17904097, ECO:0000269|PubMed:21439084}.
CC -!- INTERACTION:
CC Q3KNS1; Q2TAC2-2: CCDC57; NbExp=3; IntAct=EBI-2860313, EBI-10961624;
CC -!- SUBCELLULAR LOCATION: Cell projection, cilium, flagellum membrane
CC {ECO:0000269|PubMed:17904097}; Multi-pass membrane protein
CC {ECO:0000255}. Endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:21439084}; Multi-pass membrane protein
CC {ECO:0000255}. Note=Localizes to the midpiece of the sperm tail.
CC {ECO:0000269|PubMed:17904097}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q3KNS1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q3KNS1-2; Sequence=VSP_061519, VSP_061520;
CC -!- TISSUE SPECIFICITY: Expressed in germ cells of the testis (at protein
CC level) (PubMed:17904097). Detected in blood lymph, colon, small
CC intestine, ovary, testis, prostate, thymus and spleen with highest
CC levels in testis (PubMed:21439084). {ECO:0000269|PubMed:17904097,
CC ECO:0000269|PubMed:21439084}.
CC -!- POLYMORPHISM: A stop codon in the gene coding for this protein at
CC position Glu-768 is responsible for functional diversity thus producing
CC a pseudogene. {ECO:0000305}.
CC -!- POLYMORPHISM: The copy number of PTCHD3 varies between individuals with
CC some individuals having no copy of the gene due to a 102,624 base pair
CC deletion spanning the PTCHD3 gene. This deletion does not appear to be
CC associated with an overt phenotype and is found in 0.6-1.6% of
CC individuals of European ancestry. {ECO:0000269|PubMed:21439084}.
CC -!- SIMILARITY: Belongs to the patched family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; JF332167; AEA72435.1; -; mRNA.
DR EMBL; AL355493; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AK126025; BAC86399.1; -; mRNA.
DR EMBL; BC107139; AAI07140.1; -; mRNA.
DR CCDS; CCDS31173.1; -. [Q3KNS1-1]
DR RefSeq; NP_001030014.2; NM_001034842.3.
DR AlphaFoldDB; Q3KNS1; -.
DR SMR; Q3KNS1; -.
DR BioGRID; 131890; 30.
DR IntAct; Q3KNS1; 4.
DR STRING; 9606.ENSP00000417658; -.
DR GlyGen; Q3KNS1; 4 sites, 1 O-linked glycan (1 site).
DR iPTMnet; Q3KNS1; -.
DR PhosphoSitePlus; Q3KNS1; -.
DR BioMuta; PTCHD3; -.
DR DMDM; 425906063; -.
DR jPOST; Q3KNS1; -.
DR PaxDb; Q3KNS1; -.
DR PeptideAtlas; Q3KNS1; -.
DR PRIDE; Q3KNS1; -.
DR DNASU; 374308; -.
DR Ensembl; ENST00000610715.1; ENSP00000478346.1; ENSG00000276595.4. [Q3KNS1-2]
DR GeneID; 374308; -.
DR KEGG; hsa:374308; -.
DR UCSC; uc001itu.3; human. [Q3KNS1-1]
DR CTD; 374308; -.
DR DisGeNET; 374308; -.
DR GeneCards; PTCHD3; -.
DR HGNC; HGNC:24776; PTCHD3.
DR MIM; 611791; gene.
DR neXtProt; NX_Q3KNS1; -.
DR PharmGKB; PA142671117; -.
DR eggNOG; KOG1934; Eukaryota.
DR HOGENOM; CLU_002359_2_2_1; -.
DR InParanoid; Q3KNS1; -.
DR OrthoDB; 210960at2759; -.
DR PhylomeDB; Q3KNS1; -.
DR TreeFam; TF331806; -.
DR PathwayCommons; Q3KNS1; -.
DR SignaLink; Q3KNS1; -.
DR BioGRID-ORCS; 374308; 12 hits in 1063 CRISPR screens.
DR ChiTaRS; PTCHD3; human.
DR GenomeRNAi; 374308; -.
DR Pharos; Q3KNS1; Tbio.
DR PRO; PR:Q3KNS1; -.
DR Proteomes; UP000005640; Chromosome 10.
DR RNAct; Q3KNS1; protein.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:UniProtKB.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-KW.
DR GO; GO:0097225; C:sperm midpiece; IDA:UniProtKB.
DR InterPro; IPR003392; Ptc/Disp.
DR InterPro; IPR000731; SSD.
DR Pfam; PF02460; Patched; 1.
DR PROSITE; PS50156; SSD; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell membrane; Cell projection; Cilium;
KW Endoplasmic reticulum; Flagellum; Glycoprotein; Membrane;
KW Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..954
FT /note="Patched domain-containing protein 3"
FT /id="PRO_0000309262"
FT TRANSMEM 139..159
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 297..317
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 383..403
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 423..443
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 447..467
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 486..506
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 520..540
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 603..623
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 804..824
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 826..846
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 858..878
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 894..914
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 927..947
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 383..540
FT /note="SSD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00199"
FT REGION 1..103
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 24..40
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 43..57
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CARBOHYD 192
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 275
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 279
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 678
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 692
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 737
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT VAR_SEQ 511..533
FT /note="SVQCFCIYTGMTLLFCYFYNITC -> ASFRQQMFLPQPKRKYCYSNYDA
FT (in isoform 2)"
FT /id="VSP_061519"
FT VAR_SEQ 534..954
FT /note="Missing (in isoform 2)"
FT /id="VSP_061520"
FT VARIANT 126
FT /note="T -> A (in dbSNP:rs12098477)"
FT /id="VAR_036918"
FT VARIANT 152
FT /note="L -> P (in dbSNP:rs6482626)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_036919"
FT VARIANT 224
FT /note="A -> G (in dbSNP:rs12098562)"
FT /id="VAR_036920"
FT VARIANT 372
FT /note="R -> K (in dbSNP:rs2152099)"
FT /id="VAR_036921"
FT VARIANT 407
FT /note="C -> G (in dbSNP:rs2484180)"
FT /id="VAR_036922"
FT VARIANT 473
FT /note="D -> G (in dbSNP:rs2429485)"
FT /evidence="ECO:0000269|PubMed:14702039,
FT ECO:0000269|PubMed:21439084"
FT /id="VAR_036923"
FT VARIANT 521
FT /note="M -> T (in dbSNP:rs2505327)"
FT /evidence="ECO:0000269|PubMed:14702039"
FT /id="VAR_036924"
FT VARIANT 584
FT /note="I -> M (in dbSNP:rs1638630)"
FT /evidence="ECO:0000269|PubMed:14702039,
FT ECO:0000269|PubMed:15489334"
FT /id="VAR_036925"
FT CONFLICT 404
FT /note="R -> G (in Ref. 3; BAC86399)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 954 AA; 107689 MW; 7028A3C233858CC1 CRC64;
MPWVEPKPRP GPEQKPKLTK PDSATGPQWY QESQESESEG KQPPPGPLAP PKSPEPSGPL
ASEQDAPLPE GDDAPPRPSM LDDAPRLPLE LDDAPLPEEE TPEPTAICRH RHRCHTDCLE
GLLSRTFQWL GWQVGAHPWI FLLAPLMLTA ALGTGFLYLP KDEEEDLEEH YTPVGSPAKA
ERRFVQGHFT TNDSYRFSAS RRSTEANFVS LLVVSYSDSL LDPATFAEVS KLDGAVQDLR
VAREKGSQIQ YQQVCARYRA LCVPPNPILY AWQVNKTLNL SSISFPAYNH GRHPLYLTGF
FGGYILGGSL GMGQLLLRAK AMRLLYYLKT EDPEYDVQSK QWLTHLLDQF TNIKNILALK
KIEVVHFTSL SRQLEFEATS VTVIPVFHLA YILIILFAVT SCFRFDCIRN KMCVAAFGVI
SAFLAVVSGF GLLLHIGVPF VIIVANSPFL ILGVGVDDMF IMISAWHKTN LADDIRERMS
NVYSKAAVSI TITTITNILA LYTGIMSSFR SVQCFCIYTG MTLLFCYFYN ITCFGAFMAL
DGKREVVCLC WLKKADPKWP SFKKFCCFPF GSVPDEHGTD IHPISLFFRD YFGPFLTRSE
SKYFVVFIYV LYIISSIYGC FHVQEGLDLR NLASDDSYIT PYFNVEENYF SDYGPRVMVI
VTKKVDYWDK DVRQKLENCT KIFEKNVYVD KNLTEFWLDA YVQYLKGNSQ DPNEKNTFMN
NIPDFLSNFP NFQHDINISS SNEIISSRGF IQTTDVSSSA KKKILLFQLR RIAEDCQIPL
MVYNQAFIYF DQYAAILEDT VRNVLVASAA MFIVSLLLIP YPLCSLWVTF AIGSVIVGVT
GFMAFWKVNL DSISMINLVI CIGFSFDFSV HISYAFVSSS QPSVNQKSVE ALYLLGYPVL
QSAISTIIGV CVLAAAKAYI FRTFFKIMFL VMIFGAAHGL IFIPVFLTFF GRFI
