SRY p.Ser88Ter
c.263C>G · rs1556370558 · VCV2431744
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
46,XY sex reversal 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (1 of 1) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6 | phastCons 0.98 |
| Overall | ||
| CADD | 33.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Ser88Ter
- Coding
- c.263C>G
- MANE Select
- NM_003140
- dbSNP
- rs1556370558
- Type
- single nucleotide variant
- Location
- chrY:2787341 (GRCh38)
- Structure
- AlphaFold pLDDT 69.01 · 10 PDB
- Residue 88
- a DNA-binding region; the 'sufficient for interaction with kpnb1' region; an α-helix
Similar variants
- 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
- SRY p.Ile68Thr Pathogenic ★ ⚠ same condition
- SRY p.Leu101Phe Likely pathogenic ★ same condition
- SRY p.Met64Ile 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-ser88ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown