Is AR p.Arg616Cys (c.1846C>T) pathogenic?

AR p.Arg616Cys (c.1846C>T) is classified Pathogenic/Likely pathogenic in AR (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-08-21). AlphaMissense: likely pathogenic (1); Absent from gnomAD v4.1; Associated with androgen insensitivity syndrome.

What condition is associated with AR p.Arg616Cys (c.1846C>T)?

AR p.Arg616Cys (c.1846C>T) is associated with androgen insensitivity syndrome, Kennedy disease (ClinVar).

How common is AR p.Arg616Cys (c.1846C>T) in the general population?

AR p.Arg616Cys (c.1846C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AR p.Arg616Cys (c.1846C>T)?

AlphaMissense predicts likely pathogenic (score 1) — an in-silico prediction, not a clinical call.

AR p.Arg616Cys

c.1846C>T · rs1555990485 · VCV434266

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely pathogenic

1 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

androgen insensitivity syndrome

Computational evidence

Protein change
AlphaMissense	1	likely pathogenic ✓ concordant with ClinVar · top 4% in AR
REVEL	0.98	strongly pathogenic-leaning
SaProt	LLR -12.05	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 1.2, phastCons 1
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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.Arg616Cys
Coding: c.1846C>T
MANE Select: NM_000044
dbSNP: rs1555990485
Type: single nucleotide variant
Location: chrX:67686087 (GRCh38)
Structure: AlphaFold pLDDT 58.85 · 95 PDB
Residue 616: the 'interaction with hipk3' region; the 'interaction with ccar1' region; a DNA-binding region; an α-helix; the 'interaction with lpxn' region; a UniProt-annotated variant site (in ais and pais); a UniProt-annotated variant site (in ais)

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.Arg616His 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
AR p.Ala688Val Pathogenic/Likely pathogenic ★★ same condition
AR p.Ala766Thr 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-arg616cys (accessed [today's date]).

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