TULP1 p.Ala245=
c.735G>A · rs554210993 · VCV2958143
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 -0.71 | GERP -3.5 |
| Overall | ||
| CADD | 7.867 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,070 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000496%
8/1,614,048 alleles · very rare
exomes 6/1,461,830 · genomes 2/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,767 |
| Admixed American | 0.00333% | 29,999 |
| European (non-Finnish) | 0.000169% | 589,998 |
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.Ala245=
- Coding
- c.735G>A
- MANE Select
- NM_003322
- dbSNP
- rs554210993
- Type
- single nucleotide variant
- Location
- chr6:35509296 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.10 · 2 PDB
- Residue 245
- the 'disordered' region; a UniProt-annotated variant site (in rp14)
Similar variants
- TULP1 p.Ala245Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
- TULP1 p.Ala245Ser Uncertain significance ★ ⚠ same residue
- TULP1 p.Ala245Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
- TULP1 p.Ala245Val 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
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-ala245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown