TULP1 p.Ser210=
c.630A>G · rs143093240 · VCV1102991
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0442%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.7 | GERP -3.1 |
| Overall | ||
| CADD | 0.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0442%
European (non-Finnish) · 521/1,180,010 alleles
Filtering AF
0.041%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0398%
Overall
0.034%
549/1,614,088 alleles · ultra-rare
exomes 532/1,461,890 · genomes 17/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0442% | 2,265 |
| Finnishnot grpmax-eligible | 0.0203% | 4,926 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| African / African-American | 0.00267% | 37,516 |
| Admixed American | 0.00167% | 59,996 |
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.Ser210=
- Coding
- c.630A>G
- MANE Select
- NM_003322
- dbSNP
- rs143093240
- Type
- single nucleotide variant
- Location
- chr6:35509722 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.10 · 2 PDB
- Residue 210
- the 'disordered' region
Similar variants
- TULP1 p.Ser210Ter Pathogenic ★★ same residue
- TULP1 p.Ser210fs Pathogenic ★★ 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-ser210 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown