TRPS1 p.Ser289=
c.867C>A · VCV3758073
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.66%, eas)
Conditions
1
trichorhinophalangeal syndrome type I
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 12 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 12.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.66%
East Asian · 296/44,870 alleles
Filtering AF
0.598%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.574%
Overall
0.0185%
299/1,614,134 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.66% | 152 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
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
- TRPS1
- Protein
- p.Ser289=
- Coding
- c.867C>A
- MANE Select
- NM_014112
- Type
- single nucleotide variant
- Location
- chr8:115619231 (GRCh38)
- Gene constraint
- LOEUF 0.114 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.12
Similar variants
- TRPS1 c.2097-2A>C Pathogenic/Likely pathogenic ★★ same condition
- TRPS1 p.Ala932Thr Pathogenic/Likely pathogenic ★★ same condition
- TRPS1 p.Ala932Val Pathogenic ★★ same condition
- TRPS1 p.Arg257Ter Pathogenic ★★ same condition
- TRPS1 p.Arg544Ter Pathogenic ★★ same condition
- TRPS1 p.Arg624Ter Pathogenic ★★ same condition
- TRPS1 p.Arg696Ter Pathogenic ★★ same condition
- TRPS1 p.Arg921Gln 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/trps1-p-ser289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown