Is ABCC5 p.Val231Met (c.691G>A) pathogenic?

ABCC5 p.Val231Met (c.691G>A) is classified Uncertain significance in ABCC5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-04). AlphaMissense: likely benign (0.0978); Very rare (popmax 0.00267%, afr).

How common is ABCC5 p.Val231Met (c.691G>A) in the general population?

ABCC5 p.Val231Met (c.691G>A) is very rare (popmax 0.00267%, afr) (gnomAD).

What do computational predictors say about ABCC5 p.Val231Met (c.691G>A)?

AlphaMissense predicts likely benign (score 0.0978) — an in-silico prediction, not a clinical call.

ABCC5 p.Val231Met

c.691G>A · VCV3991175

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0978 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0978	likely benign
REVEL	0.385	indeterminate
SaProt	LLR -8.98	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 3.2	phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 72 kb · p 6.6e-23 · regional, not allelic
Overall
CADD	20.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.00267% African / African-American · 2/74,924 alleles

Filtering AF 0.000542% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000428%

Overall 0.00118% 19/1,614,070 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,803
African / African-Americangrpmax	0.00267%	37,462
East Asian	0.00223%	44,896
Finnishnot grpmax-eligible	0.00156%	64,024
South Asian	0.0011%	91,086
European (non-Finnish)	0.00102%	98,337

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ABCC5
Protein: p.Val231Met
Coding: c.691G>A
MANE Select: NM_005688
Type: single nucleotide variant
Location: chr3:183982908 (GRCh38)
Gene constraint: LOEUF 0.455 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 78.13 · 6 PDB
Residue 231: the abc transmembrane type-1 1 domain; an α-helix

Full ABCC5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCC5 c.825+10G>A Benign ★★ same type
ABCC5 p.Cys594= Benign ★★ same type
ABCC5 p.Ala1008Ser Uncertain significance ★ ⚠ same type
ABCC5 p.Ala1150Thr Uncertain significance ★ ⚠ same type
ABCC5 p.Ala1182Val Uncertain significance ★ ⚠ same type
ABCC5 p.Ala1302Gly Uncertain significance ★ ⚠ same type
ABCC5 p.Ala1343Thr Uncertain significance ★ ⚠ same type
ABCC5 p.Ala1434Thr 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/abcc5-p-val231met (accessed [today's date]).

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