Is AR p.His690= (c.2070C>T) pathogenic?

AR p.His690= (c.2070C>T) is classified Benign in AR (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-03). Ultra-rare (popmax 0.0119%, eas); Associated with Kennedy disease.

What condition is associated with AR p.His690= (c.2070C>T)?

AR p.His690= (c.2070C>T) is associated with Kennedy disease, androgen insensitivity syndrome (ClinVar).

How common is AR p.His690= (c.2070C>T) in the general population?

AR p.His690= (c.2070C>T) is ultra-rare (popmax 0.0119%, eas) (gnomAD).

How is Kennedy disease inherited?

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

AR p.His690=

c.2070C>T · rs754583155 · VCV2932380

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0119%, eas)

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 0.12	GERP -2.1, phastCons 0.99
Overall
CADD	2.398	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0119% East Asian · 4/33,737 alleles

Filtering AF 0.00396% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00236%

Overall 0.00339% 41/1,209,699 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0119%	8,434
Admixed American	0.00437%	22,868
Remaining individualsnot grpmax-eligible	0.0042%	23,793
South Asian	0.00353%	28,340
European (non-Finnish)	0.00324%	30,866
Finnishnot grpmax-eligible	0.00215%	46,610
African / African-American	0.00175%	57,154

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.His690=
Coding: c.2070C>T
MANE Select: NM_000044
dbSNP: rs754583155
Type: single nucleotide variant
Location: chrX:67711586 (GRCh38)
Structure: AlphaFold pLDDT 58.85 · 95 PDB
Residue 690: the nr lbd domain; the 'interaction with ccar1' region; the 'interaction with kat7' region; the 'interaction with lpxn' 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 p.His690Asn Uncertain significance ★ ⚠ same residue
AR p.His690Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
AR p.His690Pro 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
AR p.Ala588Pro Pathogenic/Likely pathogenic ★★ same condition
AR p.Ala597Thr 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-his690 (accessed [today's date]).

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