Is SRY p.Ala113= (c.339A>G) pathogenic?

SRY p.Ala113= (c.339A>G) is classified Likely benign in SRY (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Absent from gnomAD v4.1; Associated with 46,XY sex reversal 1.

What condition is associated with SRY p.Ala113= (c.339A>G)?

SRY p.Ala113= (c.339A>G) is associated with 46,XY sex reversal 1 (ClinVar).

How common is SRY p.Ala113= (c.339A>G) in the general population?

SRY p.Ala113= (c.339A>G) is absent from gnomAD v4.1 (gnomAD).

SRY p.Ala113=

c.339A>G · rs773247144 · VCV752210

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

46,XY sex reversal 1

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 -11
Overall
CADD	10.71	PHRED · no single calibrated threshold — expert panels disagree

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: SRY
Protein: p.Ala113=
Coding: c.339A>G
MANE Select: NM_003140
dbSNP: rs773247144
Type: single nucleotide variant
Location: chrY:2787265 (GRCh38)
Structure: AlphaFold pLDDT 69.01 · 10 PDB
Residue 113: a DNA-binding region; the 'sufficient for interaction with kpnb1' region; a UniProt-annotated variant site (in srxy1); the 'sufficient for interaction with ep300' region; an α-helix

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

Disease context

46,XY sex reversal 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SRY p.Ala113Thr Pathogenic same residue
SRY p.Ala113Glu Likely pathogenic ★ same residue
SRY p.Ala113Val Likely pathogenic ★ same residue
SRY p.Arg76Leu Likely pathogenic ★★ same condition
SRY p.Ser155= Benign/Likely benign ★★ same condition
SRY p.Gln111Ter Pathogenic ★ same condition
SRY p.Gln57Ter Pathogenic ★ same condition
SRY p.Gly49Ter 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/sry-p-ala113 (accessed [today's date]).

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