SYP p.Pro237=
c.711C>T · VCV4950492
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0905%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.19 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.27 | GERP -3.1, phastCons 0.013 |
| Overall | ||
| CADD | 6.958 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0905%
African / African-American · 52/57,430 alleles
Filtering AF
0.0708%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0638%
Overall
0.00531%
64/1,204,496 alleles · ultra-rare
exomes 32/1,091,498 · genomes 32/112,998 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0905% | 1,104 |
| Remaining individualsnot grpmax-eligible | 0.0169% | 5,912 |
| Admixed American | 0.00657% | 15,215 |
| European (non-Finnish) | 0.000112% | 892,069 |
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
- SYP
- Protein
- p.Pro237=
- Coding
- c.711C>T
- MANE Select
- NM_003179
- Type
- single nucleotide variant
- Location
- chrX:49191668 (GRCh38)
- Structure
- AlphaFold pLDDT 77.92
Similar variants
- SYP p.Gln297Lys Uncertain significance ★★ ⚠ same type
- SYP p.Gly254Asp Uncertain significance ★★ same type
- SYP p.Ile176Val Uncertain significance ★★ ⚠ same type
- SYP p.Ala235= Benign/Likely benign ★★ same type
- SYP p.Glu62Lys Likely benign ★★ same type
- SYP p.Gly208= Likely benign ★★ same type
- SYP p.Gly227= Benign/Likely benign ★★ same type
- SYP p.Thr198Ile 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/syp-p-pro237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown