TGDS p.Ser31=
c.93A>G · VCV4749850
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0247%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.45 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 9.142 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0247%
African / African-American · 18/72,812 alleles
Filtering AF
0.0159%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0132%
Overall
0.00115%
18/1,562,306 alleles · ultra-rare
exomes 6/1,409,948 · genomes 12/152,358 · 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
- TGDS
- Protein
- p.Ser31=
- Coding
- c.93A>G
- MANE Select
- NM_014305
- Type
- single nucleotide variant
- Location
- chr13:94593901 (GRCh38)
- Gene constraint
- LOEUF 1.184 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.42
Similar variants
- TGDS c.313+1G>A Pathogenic/Likely pathogenic ★★ same type
- TGDS p.Ala100Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- TGDS p.Asn60Lys Uncertain significance ★★ ⚠ same type
- TGDS p.His103Leu Uncertain significance ★★ ⚠ same type
- TGDS p.Leu96Ile Uncertain significance ★★ ⚠ same type
- TGDS p.Val35Ile Uncertain significance ★★ ⚠ same type
- TGDS c.223-73C>T Benign ★★ same type
- TGDS c.313+19T>A Benign/Likely benign ★★ same type
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/tgds-p-ser31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown