VPS37C

VPS37C subunit of ESCRT-I, the group of ESCRT-I

Basic information

Region (hg38): 11:61130257-61161615

Links

ENSG00000167987 ∙ NCBI:55048 ∙ OMIM:610038 ∙ HGNC:26097 ∙ Uniprot:A5D8V6 ∙ 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 VPS37C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS37C 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						0
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in VPS37C

This is a list of pathogenic ClinVar variants found in the VPS37C region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61131872-G-A		not specified	Uncertain significance (May 23, 2024)
11-61131873-C-T		not specified	Uncertain significance (Jul 09, 2024)
11-61131948-G-T		not specified	Uncertain significance (Nov 03, 2022)
11-61131950-A-G		not specified	Likely benign (Aug 08, 2022)
11-61131981-G-C		not specified	Uncertain significance (Sep 10, 2024)
11-61132019-C-G		not specified	Uncertain significance (Sep 11, 2024)
11-61132059-T-C		not specified	Uncertain significance (Nov 03, 2023)
11-61132112-G-C		not specified	Uncertain significance (Dec 15, 2022)
11-61132121-G-A		not specified	Uncertain significance (Sep 08, 2024)
11-61132190-T-G		not specified	Uncertain significance (Sep 07, 2022)
11-61132209-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-61132235-G-T		not specified	Uncertain significance (Jul 26, 2024)
11-61132256-G-A		not specified	Uncertain significance (Dec 16, 2021)
11-61132278-G-A		not specified	Uncertain significance (Nov 24, 2024)
11-61132307-G-A		not specified	Uncertain significance (Oct 10, 2023)
11-61132313-T-C		not specified	Uncertain significance (May 31, 2023)
11-61132332-T-G		not specified	Uncertain significance (Dec 10, 2024)
11-61132353-C-T		not specified	Uncertain significance (Nov 09, 2022)
11-61132364-G-A		not specified	Uncertain significance (Sep 30, 2024)
11-61132368-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-61132386-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-61132416-T-C		not specified	Uncertain significance (Oct 04, 2024)
11-61132440-C-T		not specified	Uncertain significance (Feb 04, 2022)
11-61132452-G-A		not specified	Uncertain significance (Sep 22, 2023)
11-61132493-A-G		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS37C	protein_coding	protein_coding	ENST00000301765	4	31362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0382	0.932	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0142	167	166	1.00	0.0000104	2200
Missense in Polyphen		70	68.752	1.0182		823
Synonymous	0.332	68	71.6	0.950	0.00000428	774
Loss of Function	1.89	4	10.6	0.376	4.52e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.000262	0.000261
Other	0.000163	0.000163

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. {ECO:0000269|PubMed:15509564}.
• 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: 0.100

Intolerance Scores

• loftool: 0.371
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.79

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.593
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0796

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vps37c

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
• Molecular function: protein binding;calcium-dependent protein binding