XK p.Phe212=
c.636C>T · VCV4887491
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0141%, sas)
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 1.8 | GERP 0.89, phastCons 1 |
| Overall | ||
| CADD | 9.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0141%
South Asian · 8/56,762 alleles
Filtering AF
0.00694%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00506%
Overall
0.00107%
13/1,209,318 alleles · ultra-rare
exomes 10/1,097,947 · genomes 3/111,371 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0141% | 7,095 |
| African / African-American | 0.00878% | 11,393 |
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.Phe212=
- Coding
- c.636C>T
- MANE Select
- NM_021083
- Type
- single nucleotide variant
- Location
- chrX:37727763 (GRCh38)
- Structure
- AlphaFold pLDDT 81.89 · 1 PDB
- Residue 212
- a UniProt-annotated variant site (in mclds)
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-phe212 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown