MVB12A

multivesicular body subunit 12A, the group of ESCRT-I

Basic information

Region (hg38): 19:17405722-17433724

Previous symbols: [ "FAM125A" ]

Links

ENSG00000141971 ∙ NCBI:93343 ∙ ∙ HGNC:25153 ∙ Uniprot:Q96EY5 ∙ 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 MVB12A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MVB12A 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	2		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	22	2	0

Variants in MVB12A

This is a list of pathogenic ClinVar variants found in the MVB12A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17406017-A-AGGGCCTGAGTCTGGGGGCG		Human immunodeficiency virus type 1, rapid progression to AIDS	association (-)
19-17420176-G-A		not specified	Uncertain significance (Jan 10, 2022)
19-17420221-G-A		not specified	Uncertain significance (Jun 21, 2023)
19-17420223-G-C		not specified	Uncertain significance (Jun 10, 2022)
19-17420319-T-G		not specified	Uncertain significance (Sep 21, 2023)
19-17420344-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-17420344-G-C		not specified	Uncertain significance (Oct 04, 2024)
19-17420362-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-17420407-T-G		not specified	Uncertain significance (Jan 30, 2024)
19-17420570-G-C		not specified	Uncertain significance (Aug 12, 2021)
19-17420574-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-17420625-A-G		not specified	Uncertain significance (Aug 15, 2023)
19-17422395-C-T		not specified	Likely benign (Sep 15, 2021)
19-17422412-C-T		not specified	Uncertain significance (Dec 02, 2022)
19-17422413-G-A		not specified	Uncertain significance (Mar 31, 2024)
19-17422422-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-17423503-T-C		not specified	Uncertain significance (Sep 26, 2023)
19-17423551-T-G		not specified	Uncertain significance (Aug 20, 2023)
19-17423556-A-G		not specified	Uncertain significance (Dec 04, 2024)
19-17423563-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-17423582-G-T		not specified	Uncertain significance (Apr 27, 2023)
19-17423587-G-T		not specified	Uncertain significance (Apr 25, 2022)
19-17423604-G-C		not specified	Likely benign (Jul 05, 2024)
19-17423607-A-G		not specified	Likely benign (May 24, 2024)
19-17423614-C-T		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MVB12A	protein_coding	protein_coding	ENST00000317040	9	28003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000802	0.764	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.202	167	160	1.04	0.00000878	1724
Missense in Polyphen		64	60.383	1.0599		675
Synonymous	0.921	59	68.7	0.859	0.00000376	584
Loss of Function	1.19	10	15.0	0.667	8.84e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000262	0.000262
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.0000486	0.0000462
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000219	0.000217
South Asian	0.000328	0.000327
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 the ligand-mediated internalization and down- regulation of EGF receptor. {ECO:0000269|PubMed:16895919}.
• 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)

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.0916
• hipred: N
• hipred_score: 0.457
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mvb12a

Gene ontology

• Biological process: protein transport;endosomal transport;macroautophagy;viral life cycle;virus maturation;multivesicular body assembly;viral budding via host ESCRT complex;regulation of epidermal growth factor receptor signaling pathway;ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway;viral budding
• Cellular component: ESCRT I complex;nucleoplasm;Golgi apparatus;centrosome;cytosol;endosome membrane;late endosome membrane;vesicle;extracellular exosome
• Molecular function: protein binding;lipid binding;SH3 domain binding;ubiquitin binding