Gene Gene information from NCBI Gene database.
Entrez ID 55187
Gene name Vacuolar protein sorting 13 homolog D
Gene symbol VPS13D
Synonyms (NCBI Gene)
BLTP5DSCA24SCAR4SCASI
Chromosome 1
Chromosome location 1p36.22-p36.21
Summary This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While se
SNPs SNP information provided by dbSNP.
10
SNP ID Visualize variation Clinical significance Consequence
rs746736545 C>T Pathogenic Coding sequence variant, missense variant
rs756025227 C>A,G,T Pathogenic Stop gained, synonymous variant, coding sequence variant, missense variant
rs779850187 C>A,T Likely-pathogenic Coding sequence variant, missense variant
rs1557478316 G>A Pathogenic Coding sequence variant, missense variant
rs1557680710 C>T Pathogenic Stop gained, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
386
miRTarBase ID miRNA Experiments Reference
MIRT021825 hsa-miR-132-3p Microarray 17612493
MIRT022025 hsa-miR-128-3p Microarray 17612493
MIRT025941 hsa-miR-7-5p Microarray 19073608
MIRT051432 hsa-let-7e-5p CLASH 23622248
MIRT038671 hsa-miR-10a-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
8
GO ID Ontology Definition Evidence Reference
GO:0005739 Component Mitochondrion HTP 34800366
GO:0006623 Process Protein targeting to vacuole IBA
GO:0006869 Process Lipid transport IEA
GO:0007005 Process Mitochondrion organization IBA
GO:0007005 Process Mitochondrion organization IMP 29307555, 29604224
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608877 23595 ENSG00000048707
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q5THJ4
Protein name Intermembrane lipid transfer protein VPS13D (Vacuolar protein sorting-associated protein 13D)
Protein function Mediates the transfer of lipids between membranes at organelle contact sites (By similarity). Functions in promoting mitochondrial clearance by mitochondrial autophagy (mitophagy), also possibly by positively regulating mitochondrial fission (Pu
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF12624 Chorein_N 2 116 N-terminal region of Chorein or VPS13 Family
PF16908 VPS13 136 358 Vacuolar sorting-associated protein 13, N-terminal Family
PF16910 VPS13_mid_rpt 613 774 Repeating coiled region of VPS13 Repeat
PF16910 VPS13_mid_rpt 782 901 Repeating coiled region of VPS13 Repeat
PF00627 UBA 2637 2673 UBA/TS-N domain Domain
PF06650 SHR-BD 3276 3560 SHR-binding domain of vacuolar-sorting associated protein 13 Family
PF16909 VPS13_C 3982 4130 Vacuolar-sorting-associated 13 protein C-terminal Family
Tissue specificity TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:15498460}.
Sequence
MLEGLVAWVLNTYLGKYVNNLNTDQLSVALLKGAVELENLPLKKDALKELELPFEVKAGF
IGKVTLQIPFYRPHVDPWVISISSLHLIGAPEKIQDFNDEKEKLLERERKKALLQA
LEEK
WKNDRQQKGESYWYSVTASVVTRIVENIELKIQDVHLRFEDGVTNPSHPFAFGICIKNVS
MQNAVNEPVQKLMRKKQLDVAEFSIYWDVDCTLLGDLPQMELQEAMARSMESRSHHYVLE
PVFASALLKRNCSKKPLRSRHSPRIDCDIQLETIPLKLSQLQYRQIMEFLKELERKERQV
KFRRWKPKVAISKNCREWWYFALNANLYEIREQRKRCTWDFMLHRARDAVSYTDKYFN
KL
KGGLLSTDDKEEMCRIEEEQSFEELKILRELVHDRFHKQEELAESLREPQFDSPGACPGA
PEPGGGSGMLQYLQSWFPGWGGWYGQQTPEGNVVEGLSAEQQEQWIPEEILGTEEFFDPT
ADASCMNTYTKRDHVFAKLNLQLQRGTVTLLHKEQGTPQMNESAFMQLEFSDVKLLAESL
PRRNSSLLSVRLGGLFLRDLATEGTMFPLLVFPNPQKEVGRVSQSFGLQTTSADRSDHYP
AADPDGPVFEMLYERNPAHSHFERRLNVSTRPLNIIYNPQAIKKVADFFYKGKVHTSGFG
YQSELELRVAEAARRQYNKLKMQTKAEIRQTLDRLLVGDFIEESKRWTVRLDISAPQVIF
PDDFKFKNPVLVVVDLGRMLLTNTQDNSRRKSRDGSASEETQFSDDEYKTPLAT
PPNTPP
PESSSSNGEKTPPFSGVEFSEEQLQAHLMSTKMYERYSLSFMDLQIMVGRVKDNWKHVQD
IDVGPTHVVEKFNVHLQLERRLIYTSDPKYPGAVLSGNLPDLKIHINEDKISALKNCFAL
L
TTPEMKTSDTQIKEKIFPQEEQRGSLQDSVMNLTQSIVLLEQHTREVLVESQLLLAEFK
VNCMQLGVESNGRYISVLKVFGTNAHFVKRPYDAEVSLTVHGLLLVDTMQTYGADFDLLM
ASHKNLSFDIPTGSLRDSRAQSPVSGPNVAHLTDGATLNDRSATSVSLDKILTKEQESLI
KLEYQFVSSECPSMNLDSTLQVISLQVNNLDIILNPETIVELIGFLQKSFPKEKDDLSPQ
PLMTDFERSFREQGTYQSTYEQNTEVAVEIHRLNLLLLRTVGMANREKYGRKIATASIGG
TKVNVSMGSTFDMNGSLGCLQLMDLTQDNVKNQYVVSIGNSVGYENIISDIGYFESVFVR
MEDAALTEALSFTFVERSKQECFLNLKMASLHYNHSAKFLKELTLSMDELEENFRGMLKS
AATKVTTVLATKTAEYSEMVSLFETPRKTREPFILEENEIYGFDLASSHLDTVKLILNIN
IESPVVSIPRKPGSPELLVGHLGQIFIQNFVAGDDESRSDRLQVEIKDIKLYSLNCTQLA
GREAVGSEGSRMFCPPSGSGSANSQEEAHFTRHDFFESLHRGQAFHILNNTTIQFKLEKI
PIERESELTFSLSPDDLGTSSIMKIEGKFVNPVQVVLAKHVYEQVLQTLDNLVYSEDLNK
YPASATSSPCPDSPLPPLSTCGESSVERKENGLFSHSSLSNTSQKSLSVKEVKSFTQIQA
TFCISELQVQLSGDLTLGAQGLVSLKFQDFEVEFSKDHPQTLSIQIALHSLLMEDLLEKN
PDSKYKNLMVSRGAPKPSSLAQKEYLSQSCPSVSNVEYPDMPRSLPSHMEEAPNVFQLYQ
RPTSASRKKQKEVQDKDYPLTPPPSPTVDEPKILVGKSKFDDSLVHINIFLVDKKHPEFS
SSYNRVNRSIDVDFNCLDVLITLQTWVVILDFFGIGSTADNHAMRLPPEGILHNVKLEPH
ASMESGLQDPVNTKLDLKVHSLSLVLNKTTSELAKANVSKLVAHLEMIEGDLALQGSIGS
LSLSDLTCHGEFYRERFTTSGEEALIFQTFKYGRPDPLLRREHDIRVSLRMASVQYVHTQ
RFQAEVVAFIQHFTQLQDVLGRQRAAIEGQTVRDQAQRCSRVLLDIEAGAPVLLIPESSR
SNNLIVANLGKLKVKNKFLFAGFPGTFSLQDKESVPSASPTGIPKHSLRKTTSTEEPRGT
HSQGQFTMPLAGMSLGSLKSEFVPSTSTKQQGPQPTLSVGQESSSPEDHVCLLDCVVVDL
QDMDIFAAERHPREYSKAPEDSSGDLIFPSYFVRQTGGSLLTEPCRLKLQVERNLDKEIS
HTVPDISIHGNLSSVHCSLDLYKYKLIRGLLENNLGEPIEEFMRPYDLQDPRIHTVLSGE
VYTCMCFLIDMVNVSLELKDPKRKEGAGSLARFDFKKCKLLYESFSNQTKSINLVSHSMM
AFDTRYAGQKTSPGMTNVFSCIFQPAKNSSTTQGSIQIELHFRSTKDSSCFTVVLNNLRV
FLIFDWLLLVHDFLHTPSDIKKQNHVTPSRHRNSSSESAIVPKTVKSGVVTKRSSLPVSN
ERHLEVKVNVTGTEFVVIEDVSCFDTNAIILKGTTVLTYKPRFVDRPFSGSLFGIEVFSC
RLGNEHDTALSIVDPVQIQMELVGNSSYQNSSGLMDAFNSEDFPPVLEIQLQALDIRLSY
NDVQLFLAIAKSIPEQANAAVPDSVALESDSVGTYLPGASRVGEEIREGTRHTLDPVLEL
QLARLQELGFSMDDCRKALLACQGQLKKAASWL
FKNAEPLKSLSLASTSRDSPGAVAAPL
ISGVEIKAESVCICFIDDCMDCDVPLAELTFSRLNFLQRVRTSPEGYAHFTLSGDYYNRA
LSGWEPFIEPWPCSVSWQQQAASRLHPPRLKLEAKAKPRLDINITSVLIDQYVSTKESWM
ADYCKDDKDIESAKSEDWMGSSVDPPCFGQSLPLVYLRTRSTASLTNLEHQIYARAEVKT
PKRRQPFVPFALRNHTGCTLWFATLTTTPTRAALSHSGSPGVVPEGNGTFLDDTHNVSEW
REVLTGEEIPFEFEARGKLRHRHTHDLRIHQLQVRVNGWEQVSPVSVDKVGTFFRYAAPD
KNSSSSTIGSPSSRTNIIHPQVYFSSLPPVRVVFAVTMEGSARKVITVRSALIVRNRLET
PMELRLDSPSAPDKPVVLPAIMPGDSFAVPLHLTSWRLQARPKGLGVFFCKAPIHWTNVV
KTAEISSSKRECHSMDTEKSRFFRFCVAIKKENYPDYMPSNIFSDSAKQIFRQPGHTIYL
LPTVVICNLLPCELDFYVKGMPINGTLKPGKEAALHTADTSQNIELGVSLENFPLCKELL
IPPGTQNYMVRMRLYDVNRRQLNLTIRIVCRAEGSLKIFISAPYWLINKTGLPLIFRQDN
AKTDAAGQFEEHELARSLSPLLFCYADKEQPNLCTMRIGRGIHPEGMPGWCQGFSLDGGS
GVRALKVIQQGNRPGLIYNIGIDVKKGRGRYIDTCMVIFAPRYLLDNKSSHKLAFAQREF
ARGQGTANPEGYISTLPGSSVVFHWPRNDYDQLLCVRLMDVPNCIWSGGFEVNKNNSFHI
NMRDTLGKCFFLRVEITLRGATYRISFSDTDQLPPPFRIDNFSKVPVVFTQHGVAEPRLR
TEVKPMTSLDYAWDEPTLPP
FITLTVKGAGSSEINCNMNDFQDNRQLYYENFIYIAATYT
FSGLQEGTGRPVASNKAITCAELVLDVSPKTQRVILKKKEPGKRSQLWRMTGTGMLAHEG
SSVPHNPNKPSAARSTEGSAILDIAGLAAVTDNRYEPLMLRKPDRRRSTTQTWSFREGKL
TCGLHGLVVQAKGGLSGLFDGAEVVLGPDTSMELLGPVPPEQQFINQKMRPGSGMLSIRV
IPDGPTRALQITDFCHRKSSRSYEVDELPVTEQELQKLKNPDTEQELEVLVRLEGGIGLS
LINKVPEELVFASLTGINVHYTQLATSHMLELSIQDVQVDNQLIGTTQPFMLYVTPLSNE
NEVIETGPAVQVNAVKFPSKSALTNIYKHLMITAQRFTVQIEEKLLLKLLSFFGYDQAES
EVEKYDENLHEKTAEQGGTPIRYYFENLKISIPQIKLSVFTSNKLPLDLKALKSTLGFPL
IRFEDAVINLDPFTRVHPYETKEFIINDILKHFQEELLSQAARILGSVDFLGNPMGLLND
VSEGVTGLIKYGNVGGLIRNVTHGVSNSAAKFAGTLSDGLGKTMDNRHQS
EREYIRYHAA
TSGEHLVAGIHGLAHGIIGGLTSVITSTVEGVKTEGGVSGFISGLGKGLVGTVTKPVAGA
LDFASETAQAVRDTATLSGPRTQAQRVRKPRCCTGPQGLLPRYSESQAEGQEQLFKLTDN
IQDEFFIAVENIDSYCVLISSKAVYFLKSGDYVDREAIFLEVKYDDLYHCLVSKDHGKVY
VQVTKKAVSTSSGVSIPGPSHQKPMVHVKSEVLAVKLSQEINYAKSLYYEQQLMLRLSEN
REQLELDS
Sequence length 4388
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
33
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Autosomal recessive cerebellar ataxia Pathogenic rs2524405777 RCV003226138
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome Likely pathogenic; Pathogenic rs752359125, rs372431023, rs2101615505, rs202180923, rs2521537710, rs2521645799, rs2524054030, rs2524377730, rs2524078674, rs2523928931, rs1557680919, rs1557680710, rs1557684974, rs1557705968, rs1557737087
View all (6 more)
RCV001330662
RCV001726516
RCV001726517
RCV002251179
RCV002280367
View all (16 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leigh syndrome Likely pathogenic rs2521974385 RCV003110166
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spinocerebellar ataxia type 4 Likely pathogenic rs868354311 RCV004556078
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Likely benign; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Arthrogryposis multiplex congenita Uncertain significance; Conflicting classifications of pathogenicity ClinVar
Disgenet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
ATAXIA, SPINOCEREBELLAR Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATROPHIC GASTRITIS GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Asthma Asthma GWASDB_DG 24406073
★☆☆☆☆
Found in Text Mining only
Ataxia Ataxia Pubtator 29604224, 36156252 Associate
★☆☆☆☆
Found in Text Mining only
Ataxia, Spinocerebellar Spinocerebellar Ataxia BEFREE 29604224
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atrophy Atrophy Pubtator 36156252 Associate
★☆☆☆☆
Found in Text Mining only
Cataract Cataract Pubtator 31876103 Associate
★☆☆☆☆
Found in Text Mining only
Cerebellar Ataxia Cerebellar ataxia Pubtator 31876103, 36156252 Associate
★☆☆☆☆
Found in Text Mining only
Chorea Chorea Pubtator 31876103 Associate
★☆☆☆☆
Found in Text Mining only
Distal amyotrophy Distal amyotrophy HPO_DG
★☆☆☆☆
Found in Text Mining only
Dysarthria Dysarthria HPO_DG
★☆☆☆☆
Found in Text Mining only
Dystonia Dystonia Pubtator 31876103 Associate
★☆☆☆☆
Found in Text Mining only