CRTAP p.Pro43=
c.129G>A · rs764596502 · VCV2771100
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, nfe)
Conditions
1
osteogenesis imperfecta type 7
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 0.47 | GERP -3.4, phastCons 0.99 |
| Overall | ||
| CADD | 11.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
European (non-Finnish) · 47/1,176,154 alleles
Filtering AF
0.00308%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00308%
49/1,593,246 alleles · very rare
exomes 47/1,441,142 · genomes 2/152,104 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.004% | 25,025 |
| Admixed American | 0.00169% | 59,224 |
| South Asian | 0.00112% | 89,422 |
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
- CRTAP
- Protein
- p.Pro43=
- Coding
- c.129G>A
- MANE Select
- NM_006371
- dbSNP
- rs764596502
- Type
- single nucleotide variant
- Location
- chr3:33114206 (GRCh38)
- Gene constraint
- LOEUF 1.251 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.81 · 6 PDB
Similar variants
- CRTAP c.471+2C>A Pathogenic/Likely pathogenic ★★ same condition
- CRTAP p.Arg212Ter Pathogenic/Likely pathogenic ★★ same condition
- CRTAP p.Gln276Ter Pathogenic ★★ same condition
- CRTAP p.Tyr148Ter Pathogenic/Likely pathogenic ★★ same condition
- CRTAP p.Tyr340Ter Pathogenic/Likely pathogenic ★★ same condition
- CRTAP p.Tyr66Ter Pathogenic ★★ same condition
- CRTAP c.*3221C>T Uncertain significance ★★ same condition
- CRTAP c.*703A>T Uncertain significance ★★ same condition
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/crtap-p-pro43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown