VPS37B

VPS37B subunit of ESCRT-I, the group of ESCRT-I

Basic information

Region (hg38): 12:122865329-122896127

Links

ENSG00000139722 ∙ NCBI:79720 ∙ OMIM:610037 ∙ HGNC:25754 ∙ Uniprot:Q9H9H4 ∙ 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 VPS37B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS37B 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in VPS37B

This is a list of pathogenic ClinVar variants found in the VPS37B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-122867135-G-A		not specified	Uncertain significance (Feb 28, 2024)
12-122867151-G-A		not specified	Uncertain significance (Jun 19, 2024)
12-122867159-G-A		not specified	Uncertain significance (Jul 25, 2023)
12-122867164-T-A		not specified	Uncertain significance (Mar 07, 2023)
12-122867237-C-A		not specified	Uncertain significance (Dec 09, 2023)
12-122867237-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-122867267-G-T		not specified	Uncertain significance (Feb 14, 2023)
12-122867277-C-T		not specified	Uncertain significance (May 09, 2022)
12-122867300-G-A		not specified	Uncertain significance (Feb 07, 2023)
12-122867309-G-A		not specified	Uncertain significance (Jan 30, 2024)
12-122867324-C-T		not specified	Uncertain significance (Oct 03, 2022)
12-122867336-G-A		not specified	Uncertain significance (Mar 01, 2023)
12-122867345-G-C		not specified	Uncertain significance (Nov 27, 2023)
12-122867351-G-A		not specified	Uncertain significance (Nov 27, 2023)
12-122867351-G-T		not specified	Uncertain significance (May 06, 2024)
12-122867414-G-A		not specified	Uncertain significance (Jun 02, 2023)
12-122867415-C-T		not specified	Uncertain significance (Jun 21, 2021)
12-122867441-G-C		not specified	Uncertain significance (Mar 28, 2024)
12-122867459-G-T		not specified	Uncertain significance (May 15, 2024)
12-122867558-A-G		not specified	Uncertain significance (Jan 16, 2024)
12-122867591-A-T		not specified	Uncertain significance (Jul 12, 2022)
12-122867596-C-G		not specified	Uncertain significance (May 09, 2023)
12-122867598-C-G		not specified	Uncertain significance (May 29, 2024)
12-122870928-A-G		not specified	Uncertain significance (Nov 01, 2022)
12-122870970-G-A		not specified	Uncertain significance (Oct 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS37B	protein_coding	protein_coding	ENST00000267202	4	31110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0583	0.926	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.176	176	170	1.04	0.0000101	1798
Missense in Polyphen		59	56.568	1.043		633
Synonymous	-0.372	77	73.0	1.06	0.00000443	607
Loss of Function	2.10	4	11.8	0.339	5.85e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000698	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000802	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
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. {ECO:0000269|PubMed:15218037}.
• 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: 0.103

Intolerance Scores

• loftool: 0.332
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.139
• hipred: Y
• hipred_score: 0.701
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.880

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vps37b

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;positive regulation of viral release from host cell;positive regulation of viral budding via host ESCRT complex
• Cellular component: ESCRT I complex;cytoplasm;endosome;plasma membrane;endosome membrane;midbody;late endosome membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: protein binding;calcium-dependent protein binding