CASP14 p.Ala58=
c.174C>T · rs61755277 · VCV770655
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.469%, nfe)
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 -3 | GERP -2.9 |
| Overall | ||
| CADD | 10.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.469%
European (non-Finnish) · 5,539/1,180,006 alleles
Filtering AF
0.459%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.455%
Overall
0.382%
6,163/1,614,062 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.469% | 213 |
| Remaining individualsnot grpmax-eligible | 0.299% | 334 |
| South Asian | 0.254% | 394 |
| Admixed American | 0.178% | 561 |
| Finnishnot grpmax-eligible | 0.0812% | 1,231 |
| Middle Eastern | 0.066% | 1,516 |
| African / African-American | 0.0533% | 1,875 |
| East Asian | 0.00446% | 22,437 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
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
- CASP14
- Protein
- p.Ala58=
- Coding
- c.174C>T
- MANE Select
- NM_012114
- dbSNP
- rs61755277
- Type
- single nucleotide variant
- Location
- chr19:15053628 (GRCh38)
- Gene constraint
- LOEUF 1.217 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.44
Similar variants
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- CASP14 c.404-151A>C Benign ★★ same type
- CASP14 c.404-271T>C Benign ★★ same type
- CASP14 c.520+77T>C Benign ★★ same type
- CASP14 c.625-34G>T Benign ★★ same type
- CASP14 c.-46-101T>A Benign ★★ same type
- CASP14 c.-46-259A>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/casp14-p-ala58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown