Is AR p.Gln80= (c.240A>G) pathogenic?

AR p.Gln80= (c.240A>G) is classified Likely benign in AR (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-04). Ultra-rare (popmax 0.0409%, amr); Associated with androgen insensitivity syndrome.

What condition is associated with AR p.Gln80= (c.240A>G)?

AR p.Gln80= (c.240A>G) is associated with androgen insensitivity syndrome, Kennedy disease (ClinVar).

How common is AR p.Gln80= (c.240A>G) in the general population?

AR p.Gln80= (c.240A>G) is ultra-rare (popmax 0.0409%, amr) (gnomAD).

AR p.Gln80=

c.240A>G · rs867607173 · VCV2066510

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0409%, amr)

Conditions

androgen insensitivity syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Overall
CADD	3.336	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0409% Admixed American · 13/31,783 alleles

Filtering AF 0.0241% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0192%

Overall 0.00281% 29/1,032,499 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0409%	2,445
Ashkenazi Jewishnot grpmax-eligible	0.00562%	17,786
South Asian	0.00421%	23,772
East Asian	0.00367%	27,244
Finnishnot grpmax-eligible	0.00267%	37,495
European (non-Finnish)	0.00141%	70,833

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.Gln80=
Coding: c.240A>G
MANE Select: NM_000044
dbSNP: rs867607173
Type: single nucleotide variant
Location: chrX:67545386 (GRCh38)
Structure: AlphaFold pLDDT 58.85 · 95 PDB
Residue 80: the 'interaction with znf318' region; the 'modulating' region; the 'disordered' region

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

Disease context

androgen insensitivity syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Kennedy disease

Similar variants

AR p.Gln80del Benign/Likely benign ★★ same residue
AR p.Gln80dup Benign/Likely benign ★★ same residue
AR p.Gln80_Glu81insGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGln Pathogenic ★ same residue
AR p.Gln80_Glu81insGlnGlnGlnTer Pathogenic ★ same residue
AR p.Gln80_Glu81insGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGln Pathogenic same residue
AR c.1768+2T>C Pathogenic/Likely pathogenic ★★ same condition
AR c.1769-11T>A Pathogenic ★★ same condition
AR c.2450-6C>G Pathogenic ★★ same condition

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-gln80 (accessed [today's date]).

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