XK p.Phe14=
c.42C>T · VCV4688280
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00435%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.3 | GERP -2.1, phastCons 0.98 |
| Overall | ||
| CADD | 13.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00435%
Admixed American · 2/45,966 alleles
Filtering AF
0.000721%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00027%
Overall
0.000248%
3/1,208,224 alleles · very rare
exomes 3/1,093,624 · genomes 0/114,600 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00435% | 22,983 |
| European (non-Finnish) | 0.000112% | 894,158 |
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
- XK
- Protein
- p.Phe14=
- Coding
- c.42C>T
- MANE Select
- NM_021083
- Type
- single nucleotide variant
- Location
- chrX:37686003 (GRCh38)
- Structure
- AlphaFold pLDDT 81.89 · 1 PDB
Similar variants
- XK p.Arg133Ter Pathogenic ★★ same type
- XK p.Arg222Ter Pathogenic/Likely pathogenic ★★ same type
- XK p.Arg138Trp Uncertain significance ★★ ⚠ same type
- XK p.Asn244Ser Uncertain significance ★★ ⚠ same type
- XK p.Glu265Gly Uncertain significance ★★ ⚠ same type
- XK p.Leu185Ser Uncertain significance ★★ ⚠ same type
- XK p.Ser115Pro Uncertain significance ★★ ⚠ same type
- XK p.Ser415Ala 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/xk-p-phe14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown