CRTAP p.Arg78=
c.234C>G · rs2471561516 · VCV2730846
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,552,488)
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 0.19 | GERP -3.7, phastCons 0.97 |
| Overall | ||
| CADD | 12.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,552,488). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CRTAP
- Protein
- p.Arg78=
- Coding
- c.234C>G
- MANE Select
- NM_006371
- dbSNP
- rs2471561516
- Type
- single nucleotide variant
- Location
- chr3:33114311 (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 78
- an α-helix
Similar variants
- CRTAP p.Arg78His 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-arg78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown