Is SRY p.Ser155= (c.465C>T) pathogenic?

SRY p.Ser155= (c.465C>T) is classified Benign/Likely benign in SRY (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-06). Absent from gnomAD v4.1; Associated with 46,XY sex reversal 1.

What condition is associated with SRY p.Ser155= (c.465C>T)?

SRY p.Ser155= (c.465C>T) is associated with 46,XY sex reversal 1 (ClinVar).

How common is SRY p.Ser155= (c.465C>T) in the general population?

SRY p.Ser155= (c.465C>T) is absent from gnomAD v4.1 (gnomAD).

SRY p.Ser155=

c.465C>T · rs11575897 · VCV703672

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

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 -3.2
Overall
CADD	5.128	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.Ser155=
Coding: c.465C>T
MANE Select: NM_003140
dbSNP: rs11575897
Type: single nucleotide variant
Location: chrY:2787139 (GRCh38)
Structure: AlphaFold pLDDT 69.01 · 10 PDB
Residue 155: the 'necessary for interaction with znf208 isoform krab-o' region

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.Arg76Leu Likely pathogenic ★★ same condition
SRY p.Gln111Ter Pathogenic ★ same condition
SRY p.Gln57Ter Pathogenic ★ same condition
SRY p.Gly49Ter Pathogenic ★ same condition
SRY p.Ile68Thr Pathogenic ★ ⚠ same condition
SRY p.Leu101Phe Likely pathogenic ★ same condition
SRY p.Met64Ile Likely pathogenic ★ same condition
SRY p.Ser71Tyr 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/sry-p-ser155 (accessed [today's date]).

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