TULP1 p.Pro59=
c.177C>G · rs2150928740 · VCV1603298
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000191%, nfe)
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 0.4 | GERP -1.2, phastCons 0.61 |
| Overall | ||
| CADD | 10.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000191%
European (non-Finnish) · 2/1,046,378 alleles
Filtering AF
3.2e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.2e-05%
Overall
0.000149%
2/1,343,392 alleles · very rare
exomes 2/1,191,370 · genomes 0/152,022 · 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
- TULP1
- Protein
- p.Pro59=
- Coding
- c.177C>G
- MANE Select
- NM_003322
- dbSNP
- rs2150928740
- Type
- single nucleotide variant
- Location
- chr6:35512193 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.10 · 2 PDB
- Residue 59
- the 'disordered' region
Similar variants
- TULP1 p.Pro59Leu Uncertain significance ★★ ⚠ same residue
- TULP1 p.Pro59Ser Uncertain significance ★ ⚠ same residue
- TULP1 c.1112+1G>A Likely pathogenic ★★ same type
- TULP1 c.1495+1G>A Pathogenic/Likely pathogenic ★★ same type
- TULP1 c.1496-6C>A Pathogenic/Likely pathogenic ★★ same type
- TULP1 c.718+2T>C Pathogenic ★★ same type
- TULP1 c.99+1G>A Pathogenic/Likely pathogenic ★★ same type
- TULP1 c.999+5G>C Pathogenic/Likely pathogenic ★★ 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/tulp1-p-pro59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown