KRTCAP2 p.Val103Phe
c.307G>T · rs200517433 · VCV3117165
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.03%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.147 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP -0.24, phastCons 1 |
| Regional constraint | o/e 0.95 | unconstrained · MANE · 3,781 bp · p 0.55 · regional, not allelic |
| Overall | ||
| CADD | 19.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.03%
Admixed American · 18/60,004 alleles
Filtering AF
0.0194%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.016%
Overall
0.0124%
200/1,614,016 alleles · ultra-rare
exomes 180/1,461,748 · genomes 20/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.03% | 3,334 |
| European (non-Finnish) | 0.0147% | 6,781 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| African / African-American | 0.004% | 25,006 |
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
- KRTCAP2
- Protein
- p.Val103Phe
- Coding
- c.307G>T
- MANE Select
- NM_173852
- dbSNP
- rs200517433
- Type
- single nucleotide variant
- Location
- chr1:155169544 (GRCh38)
- Gene constraint
- LOEUF 1.04 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.91 · 2 PDB
Similar variants
- KRTCAP2 c.-30G>A Uncertain significance ★ same type
- KRTCAP2 c.-35C>T Uncertain significance ★ same type
- KRTCAP2 c.-3A>G Uncertain significance ★ same type
- KRTCAP2 c.-56G>A Uncertain significance ★ same type
- KRTCAP2 c.-56G>C Uncertain significance ★ same type
- KRTCAP2 c.-57C>T Uncertain significance ★ same type
- KRTCAP2 c.-66A>G Uncertain significance ★ same type
- KRTCAP2 c.-72A>G 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/krtcap2-p-val103phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown