CRTAP p.Arg72=
c.216G>A · rs1227411759 · VCV748934
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0018%, amr)
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 1.3 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 13.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0018%
Admixed American · 1/55,584 alleles
Overall
6.38e-05%
1/1,567,860 alleles · very rare
exomes 1/1,415,610 · genomes 0/152,250 · 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
- CRTAP
- Protein
- p.Arg72=
- Coding
- c.216G>A
- MANE Select
- NM_006371
- dbSNP
- rs1227411759
- Type
- single nucleotide variant
- Location
- chr3:33114293 (GRCh38)
- Gene constraint
- LOEUF 1.251 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.81 · 6 PDB
- Residue 72
- an α-helix
Similar variants
- CRTAP p.Arg72Leu Uncertain significance ★ ⚠ same residue
- 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
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-arg72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown