XK p.Ser102fs
c.304_311del · VCV4949649
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
XK-related disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 3 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- XK
- Protein
- p.Ser102fs
- Coding
- c.304_311del
- MANE Select
- NM_021083
- Type
- Deletion
- Location
- chrX:37694343 (GRCh38)
- Structure
- AlphaFold pLDDT 81.89 · 1 PDB
Disease context
XK-related disorders
Similar variants
- XK p.Arg133Ter Pathogenic ★★ same condition
- XK p.Leu286fs Pathogenic ★★ same type
- XK c.246-9del Likely benign ★ same type
- XK p.Asn313fs Pathogenic same type
- XK p.Phe338fs Pathogenic 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-ser102fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown