Is ACAA2 p.Lys312Asn (c.936G>C) pathogenic?

ACAA2 p.Lys312Asn (c.936G>C) is classified Uncertain significance in ACAA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-07). AlphaMissense: likely benign (0.169); Very rare (popmax 0.0079%, nfe).

How common is ACAA2 p.Lys312Asn (c.936G>C) in the general population?

ACAA2 p.Lys312Asn (c.936G>C) is very rare (popmax 0.0079%, nfe) (gnomAD).

What do computational predictors say about ACAA2 p.Lys312Asn (c.936G>C)?

AlphaMissense predicts likely benign (score 0.169) — an in-silico prediction, not a clinical call.

ACAA2 p.Lys312Asn

c.936G>C · rs539036880 · VCV2215967

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.169 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0079%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.169	likely benign
REVEL	0.315	indeterminate
SaProt	LLR -8.80	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 0.097	phastCons 0.93
Regional constraint	o/e 0.97	unconstrained · MANE · 30 kb · p 0.51 · regional, not allelic
Overall
CADD	15.95	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 0.0079% European (non-Finnish) · 85/1,076,504 alleles

Filtering AF 0.00653% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00602%

Overall 0.00618% 88/1,423,258 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0079%	12,665
Remaining individualsnot grpmax-eligible	0.00366%	27,306
African / African-American	0.00151%	66,272

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: ACAA2
Protein: p.Lys312Asn
Coding: c.936G>C
MANE Select: NM_006111
dbSNP: rs539036880
Type: single nucleotide variant
Location: chr18:49787309 (GRCh38)
Gene constraint: LOEUF 1.148 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 97.49 · 2 PDB
Residue 312: a modified residue (n6-acetyllysine; alternate); a modified residue (n6-succinyllysine; alternate); an α-helix

Full ACAA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACAA2 p.Lys312Thr Uncertain significance ★ ⚠ same residue
ACAA2 p.Tyr198Asn Benign ★★ same type
ACAA2 p.Ala183Thr Uncertain significance ★ ⚠ same type
ACAA2 p.Ala196Thr Uncertain significance ★ ⚠ same type
ACAA2 p.Ala250Thr Uncertain significance ★ ⚠ same type
ACAA2 p.Ala267Gly Uncertain significance ★ ⚠ same type
ACAA2 p.Ala70Ser Uncertain significance ★ ⚠ same type
ACAA2 p.Arg133His 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/acaa2-p-lys312asn (accessed [today's date]).

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