VPS37D

VPS37D subunit of ESCRT-I, the group of ESCRT-I

Basic information

Region (hg38): 7:73667831-73672112

Previous symbols: [ "WBSCR24" ]

Links

ENSG00000176428 ∙ NCBI:155382 ∙ OMIM:610039 ∙ HGNC:18287 ∙ Uniprot:Q86XT2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VPS37D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS37D gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	26	2	1

Variants in VPS37D

This is a list of pathogenic ClinVar variants found in the VPS37D region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-73667969-C-T		not specified	Uncertain significance (Dec 13, 2022)
7-73667992-G-A		not specified	Uncertain significance (May 30, 2024)
7-73669441-G-A		not specified	Uncertain significance (Jun 10, 2024)
7-73669468-C-T		not specified	Uncertain significance (Dec 18, 2023)
7-73669480-A-T		not specified	Uncertain significance (Mar 24, 2023)
7-73669495-G-A		not specified	Uncertain significance (Jan 31, 2022)
7-73669500-C-A		not specified	Uncertain significance (Dec 15, 2023)
7-73669530-A-G		not specified	Uncertain significance (Aug 12, 2021)
7-73669534-A-G		not specified	Uncertain significance (Jun 01, 2023)
7-73669559-C-T			Benign (Jul 01, 2024)
7-73669570-C-T		not specified	Uncertain significance (Dec 19, 2022)
7-73669571-G-A			Likely benign (Apr 01, 2023)
7-73671006-C-T			Likely benign (Feb 01, 2024)
7-73671023-G-C		not specified	Uncertain significance (May 31, 2023)
7-73671077-C-T		not specified	Uncertain significance (Jan 12, 2024)
7-73671083-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
7-73671086-G-A		not specified	Uncertain significance (Jun 04, 2024)
7-73671108-C-T		not specified	Uncertain significance (Sep 21, 2023)
7-73671112-G-A			Likely benign (Apr 01, 2024)
7-73671141-G-A		not specified	Uncertain significance (Apr 25, 2023)
7-73671156-C-T		not specified	Uncertain significance (Jan 11, 2023)
7-73671192-A-T		not specified	Uncertain significance (Jun 24, 2022)
7-73671197-T-C		not specified	Uncertain significance (Oct 06, 2022)
7-73671206-G-A		not specified	Uncertain significance (Mar 04, 2024)
7-73671222-C-A		not specified	Uncertain significance (Jul 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS37D	protein_coding	protein_coding	ENST00000324941	4	4288

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.916	0.0833	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.880	96	124	0.777	0.00000813	1517
Missense in Polyphen		50	67.402	0.74182		696
Synonymous	-0.553	62	56.7	1.09	0.00000349	570
Loss of Function	2.61	0	7.96	0.00	3.41e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into multivesicular bodies. May be involved in cell growth and differentiation.
• Disease: DISEASE: Note=VPS37D is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.
• Pathway: Endocytosis - Homo sapiens (human);Disease;Vesicle-mediated transport;Membrane Trafficking;Assembly Of The HIV Virion;Budding and maturation of HIV virion;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;Endosomal Sorting Complex Required For Transport (ESCRT);Infectious disease;Membrane binding and targetting of GAG proteins;Synthesis And Processing Of GAG, GAGPOL Polyproteins (Consensus)

Recessive Scores

• pRec: 0.113

Haploinsufficiency Scores

• pHI: 0.173
• hipred: Y
• hipred_score: 0.704
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.640

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vps37d
• Phenotype: vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: protein targeting to membrane;protein targeting to vacuole;protein transport;endosomal transport;macroautophagy;viral life cycle;endosome transport via multivesicular body sorting pathway;multivesicular body assembly;viral budding via host ESCRT complex;ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
• Cellular component: ESCRT I complex;endosome membrane;late endosome membrane;intracellular membrane-bounded organelle;extracellular exosome