Is ARMT1 p.His306Gln (c.918C>A) pathogenic?

ARMT1 p.His306Gln (c.918C>A) is classified Uncertain significance in ARMT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-12). AlphaMissense: likely benign (0.0891); Very rare (popmax 0.00333%, amr).

How common is ARMT1 p.His306Gln (c.918C>A) in the general population?

ARMT1 p.His306Gln (c.918C>A) is very rare (popmax 0.00333%, amr) (gnomAD).

What do computational predictors say about ARMT1 p.His306Gln (c.918C>A)?

AlphaMissense predicts likely benign (score 0.0891) — an in-silico prediction, not a clinical call.

ARMT1 p.His306Gln

c.918C>A · rs1266945627 · VCV2301060

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0891 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00333%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0891	likely benign
REVEL	0.041	moderately benign-leaning
SaProt	LLR -5.86	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 -2.9	GERP -4.5
Regional constraint	o/e 0.97	unconstrained · MANE · 17 kb · p 0.56 · regional, not allelic
Overall
CADD	0.007	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 0.00333% Admixed American · 2/60,018 alleles

Filtering AF 0.000553% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000207%

Overall 0.000124% 2/1,614,074 alleles · very rare exomes 2/1,461,768 · genomes 0/152,306 · joint denominator

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: ARMT1
Protein: p.His306Gln
Coding: c.918C>A
MANE Select: NM_024573
dbSNP: rs1266945627
Type: single nucleotide variant
Location: chr6:151468702 (GRCh38)
Gene constraint: LOEUF 1.083 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.36 · 2 PDB

Full ARMT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARMT1 p.Ala344Gly Uncertain significance ★ ⚠ same type
ARMT1 p.Arg24Ile Uncertain significance ★ ⚠ same type
ARMT1 p.Asn212Ser Uncertain significance ★ ⚠ same type
ARMT1 p.Asp86Asn Uncertain significance ★ ⚠ same type
ARMT1 p.Glu341Asp Uncertain significance ★ ⚠ same type
ARMT1 p.Glu341Lys Uncertain significance ★ ⚠ same type
ARMT1 p.Gly201Glu Uncertain significance ★ ⚠ same type
ARMT1 p.Gly439Asp 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/armt1-p-his306gln (accessed [today's date]).

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