KRTCAP2 p.Gly4Ser
c.10G>A · VCV3289777
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.083 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.52 | donor gain · deltas |
| Pangolin | Δ0.27 | gain · loss 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.8 | GERP 2.3, phastCons 1 |
| Regional constraint | o/e 0.95 | unconstrained · MANE · 3,781 bp · p 0.55 · regional, not allelic |
| Overall | ||
| CADD | 23.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
African / African-American · 8/74,916 alleles
Filtering AF
0.00656%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00608%
Overall
0.00644%
104/1,613,778 alleles · ultra-rare
exomes 93/1,461,582 · genomes 11/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0107% | 9,365 |
| European (non-Finnish) | 0.00788% | 12,688 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,816 |
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.Gly4Ser
- Coding
- c.10G>A
- MANE Select
- NM_173852
- Type
- single nucleotide variant
- Location
- chr1:155172887 (GRCh38)
- Gene constraint
- LOEUF 1.04 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.91 · 2 PDB
- Residue 4
- a UniProt-annotated variant site (in)
Similar variants
- KRTCAP2 p.Gly4Asp Uncertain significance ★ same residue
- 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
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-gly4ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown