Is ABCA5 p.Val356Glu (c.1067T>A) pathogenic?

ABCA5 p.Val356Glu (c.1067T>A) is classified Uncertain significance in ABCA5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-17). AlphaMissense: ambiguous (0.4728); Ultra-rare (popmax 0.0127%, amr).

How common is ABCA5 p.Val356Glu (c.1067T>A) in the general population?

ABCA5 p.Val356Glu (c.1067T>A) is ultra-rare (popmax 0.0127%, amr) (gnomAD).

What do computational predictors say about ABCA5 p.Val356Glu (c.1067T>A)?

AlphaMissense predicts ambiguous (score 0.4728) — an in-silico prediction, not a clinical call.

ABCA5 p.Val356Glu

c.1067T>A · rs139637578 · VCV3103290

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4728 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0127%, amr)

Computational evidence

Protein change
AlphaMissense	0.4728	ambiguous
REVEL	0.535	indeterminate
SaProt	LLR -5.03	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7	GERP 1.4, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 67 kb · p 0.22 · regional, not allelic
Overall
CADD	22.8	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 0.0127% Admixed American · 7/55,298 alleles

Filtering AF 0.0071% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00662%

Overall 0.00675% 108/1,599,462 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0127%	7,900
European (non-Finnish)	0.0085%	11,764
Remaining individualsnot grpmax-eligible	0.00162%	61,854

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: ABCA5
Protein: p.Val356Glu
Coding: c.1067T>A
MANE Select: NM_172232
dbSNP: rs139637578
Type: single nucleotide variant
Location: chr17:69302770 (GRCh38)
Gene constraint: LOEUF 0.97 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.12

Full ABCA5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCA5 p.Ser288Phe Uncertain significance ★★ ⚠ same type
ABCA5 c.4765+3A>G Likely benign ★★ same type
ABCA5 p.Asn190Ser Likely benign ★★ ⚠ same type
ABCA5 p.Asn768Asp Benign ★★ same type
ABCA5 p.Asp817Tyr Likely benign ★★ ⚠ same type
ABCA5 p.Gly1159Arg Likely benign ★★ ⚠ same type
ABCA5 p.Gly128= Benign/Likely benign ★★ same type
ABCA5 p.Ile1173Val Likely benign ★★ 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/abca5-p-val356glu (accessed [today's date]).

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