CALCA p.Phe106=
c.318C>T · rs142242325 · VCV785341
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1%, 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 0.42 | GERP -3, phastCons 0.01 |
| Overall | ||
| CADD | 7.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1%
African / African-American · 751/75,018 alleles
Filtering AF
0.942%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.918%
Overall
0.0544%
878/1,614,076 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1% | 100 |
| Middle Eastern | 0.116% | 865 |
| Admixed American | 0.102% | 984 |
| Remaining individualsnot grpmax-eligible | 0.0704% | 1,421 |
| South Asian | 0.00329% | 30,359 |
| European (non-Finnish) | 0.00102% | 98,332 |
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
- CALCA
- Protein
- p.Phe106=
- Coding
- c.318C>T
- MANE Select
- NM_001741
- dbSNP
- rs142242325
- Type
- single nucleotide variant
- Location
- chr11:14968907 (GRCh38)
- Gene constraint
- LOEUF 1.186 · pLI 0.13 (gnomAD)
- Structure
- AlphaFold pLDDT 64.12 · 6 PDB
- Residue 106
- a β-strand
Similar variants
- CALCA p.Ala118Val Uncertain significance ★ same type
- CALCA p.Ala11Thr Uncertain significance ★ ⚠ same type
- CALCA p.Ala31Ser Uncertain significance ★ ⚠ same type
- CALCA p.Ala47Pro Uncertain significance ★ ⚠ same type
- CALCA p.Ala47Val Uncertain significance ★ ⚠ same type
- CALCA p.Arg123Cys Uncertain significance ★ same type
- CALCA p.Arg84Gln Uncertain significance ★ ⚠ same type
- CALCA p.Arg84Pro Uncertain significance ★ ⚠ 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/calca-p-phe106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown