Is ABCB5 p.Ala941Asp (c.2822C>A) pathogenic?

ABCB5 p.Ala941Asp (c.2822C>A) is classified Uncertain significance in ABCB5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-02). AlphaMissense: likely pathogenic (0.6605); Rare (popmax 0.167%, afr).

How common is ABCB5 p.Ala941Asp (c.2822C>A) in the general population?

ABCB5 p.Ala941Asp (c.2822C>A) is rare (popmax 0.167%, afr) (gnomAD).

What do computational predictors say about ABCB5 p.Ala941Asp (c.2822C>A)?

AlphaMissense predicts likely pathogenic (score 0.6605) — an in-silico prediction, not a clinical call.

ABCB5 p.Ala941Asp

c.2822C>A · rs149344459 · VCV3122650

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6605 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.167%, afr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.6605	likely pathogenic
REVEL	0.692	pathogenic-leaning
SaProt	LLR -10.73	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.18	GERP -1.1, phastCons 0.1
Regional constraint	o/e 1.20	unconstrained · MANE · 132 kb · p 2.2e-15 · regional, not allelic
Overall
CADD	19.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.167% African / African-American · 125/75,030 alleles

Filtering AF 0.143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.134%

Overall 0.00966% 156/1,614,106 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.167%	600
Remaining individualsnot grpmax-eligible	0.0352%	2,841
Middle Eastern	0.0165%	6,062
Admixed American	0.0133%	7,501

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: ABCB5
Protein: p.Ala941Asp
Coding: c.2822C>A
MANE Select: NM_001163941
dbSNP: rs149344459
Type: single nucleotide variant
Location: chr7:20728410 (GRCh38)
Gene constraint: LOEUF 1.178 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.01
Residue 941: the abc transmembrane type-1 2 domain

Full ABCB5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCB5 p.Ala350Thr Likely benign ★★ same type
ABCB5 p.Val1209Ala Likely benign ★★ same type
ABCB5 p.Ala1112Thr Uncertain significance ★ ⚠ same type
ABCB5 p.Ala1154Gly Uncertain significance ★ ⚠ same type
ABCB5 p.Ala221Val Uncertain significance ★ ⚠ same type
ABCB5 p.Ala223Ser Uncertain significance ★ ⚠ same type
ABCB5 p.Ala327Thr Uncertain significance ★ ⚠ same type
ABCB5 p.Ala501Glu Uncertain significance ★ ⚠ same type

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/abcb5-p-ala941asp (accessed [today's date]).

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