TULP1 p.Asp124=
c.372C>T · rs147950414 · VCV1097642
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0522%, afr)
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 -8.7 | GERP -2.8 |
| Overall | ||
| CADD | 0.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0522%
African / African-American · 39/74,666 alleles
Filtering AF
0.0393%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0347%
Overall
0.00406%
65/1,600,270 alleles · ultra-rare
exomes 44/1,449,080 · genomes 21/151,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0522% | 1,915 |
| Middle Eastern | 0.0167% | 5,996 |
| Remaining individualsnot grpmax-eligible | 0.0113% | 8,854 |
| South Asian | 0.0077% | 12,995 |
| Admixed American | 0.00168% | 59,478 |
| European (non-Finnish) | 0.000852% | 117,366 |
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.Asp124=
- Coding
- c.372C>T
- MANE Select
- NM_003322
- dbSNP
- rs147950414
- Type
- single nucleotide variant
- Location
- chr6:35510988 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.10 · 2 PDB
- Residue 124
- the 'disordered' region; a UniProt-annotated variant site (in rp14)
Similar variants
- TULP1 p.Asp124Asn Uncertain significance ★★ ⚠ same residue
- TULP1 p.Asp124Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
- TULP1 p.Asp124_Glu131del Benign/Likely benign ★★ 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
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-asp124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown