Is AK2 p.Lys181Arg (c.542A>G) pathogenic?

AK2 p.Lys181Arg (c.542A>G) is classified Uncertain significance in AK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-05). AlphaMissense: likely benign (0.1069); Very rare (popmax 0.00167%, amr).

How common is AK2 p.Lys181Arg (c.542A>G) in the general population?

AK2 p.Lys181Arg (c.542A>G) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about AK2 p.Lys181Arg (c.542A>G)?

AlphaMissense predicts likely benign (score 0.1069) — an in-silico prediction, not a clinical call.

AK2 p.Lys181Arg

c.542A>G · VCV4965679

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1069 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1069	likely benign
REVEL	0.25	benign-leaning
SaProt	LLR -7.72	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.4	GERP 2.7, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 24 kb · p 0.0069 · regional, not allelic
Overall
CADD	22.6	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 0.00167% Admixed American · 1/60,004 alleles

Overall 0.000124% 2/1,613,734 alleles · very rare exomes 1/1,461,512 · genomes 1/152,222 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,004
European (non-Finnish)	8.48e-05%	1,179,709

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: AK2
Protein: p.Lys181Arg
Coding: c.542A>G
MANE Select: NM_001625
Type: single nucleotide variant
Location: chr1:33013359 (GRCh38)
Gene constraint: LOEUF 0.954 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.49 · 3 PDB
Residue 181: a modified residue (n6-acetyllysine); an α-helix

Full AK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AK2 p.Lys181Asn Benign/Likely benign ★★ same residue
AK2 c.330+5G>A Pathogenic ★★ same type
AK2 c.498+1G>A Pathogenic/Likely pathogenic ★★ same type
AK2 p.Ala182Asp Pathogenic/Likely pathogenic ★★ same type
AK2 p.Arg103Trp Pathogenic/Likely pathogenic ★★ same type
AK2 p.Arg175Pro Likely pathogenic ★★ same type
AK2 p.Met1Val Pathogenic ★★ same type
AK2 p.Ala212Thr 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/ak2-p-lys181arg (accessed [today's date]).

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