SH2D1A p.Ser110=
c.330T>C · rs2060066337 · VCV1116192
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00217%, amr)
Conditions
2
Inborn genetic diseases
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 0.39 | GERP -4.2, phastCons 1 |
| Overall | ||
| CADD | 6.374 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00217%
Admixed American · 1/45,988 alleles
Overall
8.3e-05%
1/1,204,448 alleles · very rare
exomes 1/1,090,966 · genomes 0/113,482 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SH2D1A
- Protein
- p.Ser110=
- Coding
- c.330T>C
- MANE Select
- NM_002351
- dbSNP
- rs2060066337
- Type
- single nucleotide variant
- Location
- chrX:124370304 (GRCh38)
- Structure
- AlphaFold pLDDT 84.53 · 6 PDB
- Residue 110
- a UniProt-annotated variant site (in xlp1; uncertain significance); the 'disordered' region
Similar variants
- SH2D1A c.138-1G>A Pathogenic ★★ same condition
- SH2D1A p.Arg55Ter Pathogenic ★★ same condition
- SH2D1A p.Asp2Gly Likely pathogenic ★★ ⚠ same condition
- SH2D1A p.Met1Thr Pathogenic/Likely pathogenic ★★ same condition
- SH2D1A p.Trp64Ter Pathogenic ★★ same condition
- SH2D1A p.Cys124Ser Uncertain significance ★★ ⚠ same condition
- SH2D1A p.Ser63Pro Uncertain significance ★★ ⚠ same condition
- SH2D1A p.Val102Ile Uncertain significance ★★ ⚠ 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/sh2d1a-p-ser110 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown