Is ANKMY1 p.Gln92Arg (c.275A>G) pathogenic?

ANKMY1 p.Gln92Arg (c.275A>G) is classified Likely benign in ANKMY1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-02). AlphaMissense: likely benign (0.0676); Absent from gnomAD v4.1.

How common is ANKMY1 p.Gln92Arg (c.275A>G) in the general population?

ANKMY1 p.Gln92Arg (c.275A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ANKMY1 p.Gln92Arg (c.275A>G)?

AlphaMissense predicts likely benign (score 0.0676) — an in-silico prediction, not a clinical call.

ANKMY1 p.Gln92Arg

c.275A>G · rs2092118347 · VCV2263183

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0676 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0676	likely benign
REVEL	0.027	moderately benign-leaning
SaProt	LLR -7.10	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 -3.8	GERP -0.81
Regional constraint	o/e 0.99	unconstrained · MANE · 78 kb · p 0.63 · regional, not allelic
Overall
CADD	0.105	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM Q3R vs ClinVar Q92R) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ANKMY1
Protein: p.Gln92Arg
Coding: c.275A>G
MANE Select: NM_001282771
dbSNP: rs2092118347
Type: single nucleotide variant
Location: chr2:240554927 (GRCh38)
Gene constraint: LOEUF 1.141 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.09

Full ANKMY1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANKMY1 p.Ala219= Benign ★★ same type
ANKMY1 p.His268Asn Likely benign ★★ same type
ANKMY1 p.Ser212Thr Benign ★★ same type
ANKMY1 p.Ala1014Gly Uncertain significance ★ ⚠ same type
ANKMY1 p.Ala165Val Uncertain significance ★ ⚠ same type
ANKMY1 p.Ala281Ser Uncertain significance ★ ⚠ same type
ANKMY1 p.Ala340Val Uncertain significance ★ ⚠ same type
ANKMY1 p.Ala356Val 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/ankmy1-p-gln92arg (accessed [today's date]).

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