Is AR p.Asn693Ile (c.2078A>T) pathogenic?

AR p.Asn693Ile (c.2078A>T) is classified Uncertain significance in AR (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-03). AlphaMissense: likely pathogenic (0.6705); Absent from gnomAD v4.1; Associated with partial androgen insensitivity syndrome.

What condition is associated with AR p.Asn693Ile (c.2078A>T)?

AR p.Asn693Ile (c.2078A>T) is associated with partial androgen insensitivity syndrome (ClinVar).

How common is AR p.Asn693Ile (c.2078A>T) in the general population?

AR p.Asn693Ile (c.2078A>T) is absent from gnomAD v4.1 (gnomAD).

How is Partial androgen insensitivity syndrome inherited?

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

What do computational predictors say about AR p.Asn693Ile (c.2078A>T)?

AlphaMissense predicts likely pathogenic (score 0.6705) — an in-silico prediction, not a clinical call.

AR p.Asn693Ile

c.2078A>T · rs2147524940 · VCV1333500

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6705 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

partial androgen insensitivity syndrome

Computational evidence

Protein change
AlphaMissense	0.6705	likely pathogenic
REVEL	0.589	indeterminate
SaProt	LLR -10.13	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 0.48, phastCons 1
Overall
CADD	24.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: AR
Protein: p.Asn693Ile
Coding: c.2078A>T
MANE Select: NM_000044
dbSNP: rs2147524940
Type: single nucleotide variant
Location: chrX:67711594 (GRCh38)
Structure: AlphaFold pLDDT 58.85 · 95 PDB
Residue 693: the nr lbd domain; the 'interaction with ccar1' region; a UniProt-annotated variant site (in ais); the 'interaction with kat7' region; a β-strand; the 'interaction with lpxn' region

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

Disease context

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

For Partial androgen insensitivity syndrome (Orphanet):

Inheritance: X-linked recessive
Onset: All ages

Similar variants

AR p.Asn693Lys Likely pathogenic ★ same residue
AR c.1768+2T>C Pathogenic/Likely pathogenic ★★ same condition
AR c.1769-11T>A Pathogenic ★★ same condition
AR p.Ala597Thr Pathogenic ★★ same condition
AR p.Ala871Val Pathogenic/Likely pathogenic ★★ same condition
AR p.Arg608Gln Pathogenic/Likely pathogenic ★★ same condition
AR p.Arg616His Pathogenic ★★ same condition
AR p.Arg841Cys 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-asn693ile (accessed [today's date]).

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