Is AR p.Gln80del (c.171GCA[22]) pathogenic?

AR p.Gln80del (c.171GCA[22]) is classified Benign/Likely benign in AR (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-01-28). Common (popmax 8.64%, eas) — too common for a highly-penetrant pathogenic allele; Associated with prostate cancer.

What condition is associated with AR p.Gln80del (c.171GCA[22])?

AR p.Gln80del (c.171GCA[22]) is associated with prostate cancer, hypospadias 1, X-linked, partial androgen insensitivity syndrome (ClinVar).

AR p.Gln80del

Q: How common is AR p.Gln80del (c.171GCA[22]) in the general population?

AR p.Gln80del (c.171GCA[22]) is common (popmax 8.64%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.171GCA[22] · rs3032358 · VCV464798

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Common

common (popmax 8.64%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

prostate cancer

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.6	GERP -0.24, phastCons 0.033
Overall
CADD	9.018	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	(GCA)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.64% East Asian · 2,484/28,762 alleles

Filtering AF 8.35% ClinGen BA1/BS1 input FAF95, joint · FAF99 8.24%

Overall 4.92% 48,344/981,829 alleles · common

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	12.3%	8
Amishnot grpmax-eligible	11%	9
East Asiangrpmax	8.64%	12
African / African-American	6.96%	14
Admixed American	6.79%	15
Middle Eastern	6.14%	16
Remaining individualsnot grpmax-eligible	5.96%	17
Ashkenazi Jewishnot grpmax-eligible	5.51%	18
European (non-Finnish)	4.25%	24
South Asian	3.1%	32

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Gln80del
Coding: c.171GCA[22]
MANE Select: NM_000044
dbSNP: rs3032358
Type: Microsatellite
Location: chrX:67545317 (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

prostate cancer — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hypospadias 1, X-linked partial androgen insensitivity syndrome Kennedy disease androgen insensitivity syndrome

Similar variants

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 p.Gln80= Likely benign ★ same residue
AR p.Gln80_Glu81insGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGln Pathogenic ★ same residue
AR p.Gln80_Glu81insGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGlnGln Likely benign same residue
AR p.Gly462_Gly473del Uncertain significance ★★ 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-gln80del (accessed [today's date]).

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