MVB12B

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

Basic information

Region (hg38): 9:126326829-126507041

Previous symbols: [ "C9orf28", "FAM125B" ]

Links

ENSG00000196814 ∙ NCBI:89853 ∙ ∙ HGNC:23368 ∙ Uniprot:Q9H7P6 ∙ 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 MVB12B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MVB12B 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	3	5
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				2		2
Total	0	0	16	5	3

Variants in MVB12B

This is a list of pathogenic ClinVar variants found in the MVB12B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-126326965-CCCG-C		MVB12B-related disorder	Likely benign (Aug 09, 2022)
9-126340561-G-A		MVB12B-related disorder	Benign (Oct 18, 2019)
9-126340565-A-G		not specified	Uncertain significance (Jun 05, 2023)
9-126340571-C-G		not specified	Uncertain significance (Jan 17, 2024)
9-126340601-C-T		not specified	Uncertain significance (Aug 29, 2022)
9-126340620-G-A		not specified	Uncertain significance (Sep 15, 2021)
9-126381156-A-G		MVB12B-related disorder	Benign (Oct 18, 2019)
9-126386584-T-C		not specified	Uncertain significance (Oct 20, 2023)
9-126386637-A-G		not specified	Uncertain significance (Dec 15, 2022)
9-126392124-G-A			Likely benign (Dec 01, 2022)
9-126392147-G-A		not specified	Uncertain significance (Nov 07, 2022)
9-126392176-C-G		not specified	Uncertain significance (Aug 05, 2023)
9-126395571-A-G		MVB12B-related disorder	Likely benign (Oct 28, 2019)
9-126395649-C-T		not specified	Uncertain significance (Oct 05, 2023)
9-126395650-G-A		MVB12B-related disorder	Likely benign (May 21, 2020)
9-126395688-A-C		not specified	Uncertain significance (Jul 06, 2021)
9-126395688-A-G		not specified	Uncertain significance (Jan 24, 2023)
9-126421889-G-T		not specified	Uncertain significance (Apr 18, 2023)
9-126421907-C-T		not specified	Uncertain significance (Oct 26, 2021)
9-126421915-G-A		not specified	Uncertain significance (Aug 15, 2023)
9-126481391-G-T		not specified	Uncertain significance (Jun 18, 2024)
9-126483963-G-A		MVB12B-related disorder	Likely benign (Sep 10, 2019)
9-126503167-G-A		MVB12B-related disorder	Likely benign (Jul 09, 2019)
9-126503180-G-A		not specified	Uncertain significance (May 14, 2024)
9-126503192-C-G		not specified	Uncertain significance (May 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MVB12B	protein_coding	protein_coding	ENST00000361171	10	180193

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.559	0.441	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	119	183	0.652	0.0000108	2060
Missense in Polyphen		41	68.627	0.59743		706
Synonymous	-0.249	72	69.4	1.04	0.00000450	626
Loss of Function	3.29	4	19.8	0.202	0.00000128	209

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	0.0000464	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
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.
• 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: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.825
• ghis: 0.567

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: Mvb12b

Gene ontology

• Biological process: protein transport;endosomal transport;viral life cycle;virus maturation;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;nucleus;early endosome;late endosome;cytosol;plasma membrane;endosome membrane;late endosome membrane;vesicle;extracellular exosome
• Molecular function: protein binding;lipid binding;ubiquitin binding