Is MAFB p.Ala302Val (c.905C>T) pathogenic?

MAFB p.Ala302Val (c.905C>T) is classified Likely benign in MAFB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-07-15). AlphaMissense: likely benign (0.158); Ultra-rare (popmax 0.056%, afr); Associated with Inborn genetic diseases.

What condition is associated with MAFB p.Ala302Val (c.905C>T)?

MAFB p.Ala302Val (c.905C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MAFB p.Ala302Val (c.905C>T) in the general population?

MAFB p.Ala302Val (c.905C>T) is ultra-rare (popmax 0.056%, afr) (gnomAD).

What do computational predictors say about MAFB p.Ala302Val (c.905C>T)?

AlphaMissense predicts likely benign (score 0.158) — an in-silico prediction, not a clinical call.

MAFB p.Ala302Val

c.905C>T · rs201243960 · VCV2080782

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.158 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.056%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.158	likely benign
REVEL	0.292	indeterminate
SaProt	LLR -7.97	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP -0.089, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 160 bp · p 0.44 · regional, not allelic
Overall
CADD	24.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.056% African / African-American · 42/75,066 alleles

Filtering AF 0.0425% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0378%

Overall 0.00297% 48/1,613,810 alleles · ultra-rare exomes 16/1,461,464 · genomes 32/152,346 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.056%	1,787
Remaining individualsnot grpmax-eligible	0.0048%	20,829
Admixed American	0.00333%	30,016
European (non-Finnish)	8.47e-05%	1,180,038

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MAFB
Protein: p.Ala302Val
Coding: c.905C>T
MANE Select: NM_005461
dbSNP: rs201243960
Type: single nucleotide variant
Location: chr20:40687946 (GRCh38)
Gene constraint: LOEUF 0.469 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.87

Full MAFB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MAFB p.Ser70Leu Pathogenic/Likely pathogenic ★★ same condition
MAFB p.Ala107Thr Uncertain significance ★★ ⚠ same condition
MAFB p.Ala130Val Uncertain significance ★★ ⚠ same condition
MAFB p.Ala288Val Uncertain significance ★★ ⚠ same condition
MAFB p.Asp84Glu Uncertain significance ★★ ⚠ same condition
MAFB p.His165Tyr Uncertain significance ★★ ⚠ same condition
MAFB p.His193Tyr Uncertain significance ★★ ⚠ same condition
MAFB p.Pro75Ala Uncertain significance ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mafb-p-ala302val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown