Is AR p.Gln199= (c.597G>A) pathogenic?

AR p.Gln199= (c.597G>A) is classified Likely benign in AR (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-02). Ultra-rare (popmax 0.0349%, afr); Associated with Kennedy disease.

What condition is associated with AR p.Gln199= (c.597G>A)?

AR p.Gln199= (c.597G>A) is associated with Kennedy disease, androgen insensitivity syndrome (ClinVar).

How common is AR p.Gln199= (c.597G>A) in the general population?

AR p.Gln199= (c.597G>A) is ultra-rare (popmax 0.0349%, afr) (gnomAD).

How is Kennedy disease inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

AR p.Gln199=

c.597G>A · rs746464635 · VCV2950979

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0349%, afr)

Conditions

Kennedy disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.5	GERP 0.18, phastCons 1
Overall
CADD	6.806	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0349% African / African-American · 20/57,373 alleles

Filtering AF 0.0231% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0193%

Overall 0.00215% 26/1,210,185 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0349%	2,869
Remaining individualsnot grpmax-eligible	0.00841%	11,894
Admixed American	0.00436%	22,946

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.Gln199=
Coding: c.597G>A
MANE Select: NM_000044
dbSNP: rs746464635
Type: single nucleotide variant
Location: chrX:67545743 (GRCh38)
Structure: AlphaFold pLDDT 58.85 · 95 PDB
Residue 199: 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

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

Also linked: androgen insensitivity syndrome

For Kennedy disease (Orphanet):

Inheritance: X-linked recessive
Onset: Adult
Prevalence: <1 / 1 000 000 (Italy)

Similar variants

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
AR p.Ala588Pro Pathogenic/Likely pathogenic ★★ same condition
AR p.Ala597Thr Pathogenic ★★ same condition
AR p.Ala688Val Pathogenic/Likely pathogenic ★★ same condition
AR p.Ala766Thr Pathogenic ★★ same condition
AR p.Ala871Val Pathogenic/Likely 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-gln199 (accessed [today's date]).

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