Is AR p.Val30Met (c.88G>A) pathogenic?

AR p.Val30Met (c.88G>A) is classified Uncertain significance in AR (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-15). AlphaMissense: likely pathogenic (0.8212); Very rare (popmax 0.000112%, nfe).

How common is AR p.Val30Met (c.88G>A) in the general population?

AR p.Val30Met (c.88G>A) is very rare (popmax 0.000112%, nfe) (gnomAD).

What do computational predictors say about AR p.Val30Met (c.88G>A)?

AlphaMissense predicts likely pathogenic (score 0.8212) — an in-silico prediction, not a clinical call.

AR p.Val30Met

c.88G>A · VCV3339499

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8212 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8212	likely pathogenic
REVEL	0.712	pathogenic-leaning
SaProt	LLR -7.24	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.6	GERP 2.1, phastCons 1
Overall
CADD	25.7	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 0.000112% European (non-Finnish) · 1/895,173 alleles

Overall 9.11e-05% 1/1,098,049 alleles · very rare

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: AR
Protein: p.Val30Met
Coding: c.88G>A
MANE Select: NM_000044
Type: single nucleotide variant
Location: chrX:67545234 (GRCh38)
Structure: AlphaFold pLDDT 58.85 · 95 PDB
Residue 30: the 'interaction with znf318' region; the 'modulating' region

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

Similar variants

AR c.1768+2T>C Pathogenic/Likely pathogenic ★★ same type
AR c.1769-11T>A Pathogenic ★★ same type
AR c.2450-6C>G Pathogenic ★★ same type
AR p.Ala588Pro Pathogenic/Likely pathogenic ★★ same type
AR p.Ala597Thr Pathogenic ★★ same type
AR p.Ala688Val Pathogenic/Likely pathogenic ★★ same type
AR p.Ala766Thr Pathogenic ★★ same type
AR p.Ala871Val Pathogenic/Likely pathogenic ★★ 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/ar-p-val30met (accessed [today's date]).

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