CALCR p.Glu255=
c.765G>A · rs73419385 · VCV785225
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.66%, afr) — too common for a highly-penetrant pathogenic allele
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 0.065 | GERP -4, phastCons 0.001 |
| Overall | ||
| CADD | 0.721 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.66%
African / African-American · 4,988/74,940 alleles
Filtering AF
6.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.44%
Overall
0.376%
6,070/1,613,402 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.66% | 15 |
| Middle Eastern | 0.562% | 178 |
| Remaining individualsnot grpmax-eligible | 0.548% | 183 |
| Admixed American | 0.487% | 205 |
| European (non-Finnish) | 0.0342% | 2,920 |
| South Asian | 0.00989% | 10,115 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,570 |
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
- CALCR
- Protein
- p.Glu255=
- Coding
- c.765G>A
- MANE Select
- NM_001742
- dbSNP
- rs73419385
- Type
- single nucleotide variant
- Location
- chr7:93443641 (GRCh38)
- Gene constraint
- LOEUF 1.039 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.14 · 32 PDB
- Residue 255
- a disulfide bond; an α-helix
Similar variants
- CALCR p.Val283Met Uncertain significance ★★ ⚠ same type
- CALCR c.1149+72A>G Benign ★★ same type
- CALCR c.1191+167C>A Benign ★★ same type
- CALCR c.206-113T>G Benign ★★ same type
- CALCR c.429+37T>C Benign ★★ same type
- CALCR c.51+105C>T Benign ★★ same type
- CALCR c.521+53C>T Benign ★★ same type
- CALCR c.522-1226A>G Benign ★★ 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/calcr-p-glu255 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown