NCKAP1 p.Phe97fs
c.291del · VCV4880547
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 31 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.5, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NCKAP1
- Protein
- p.Phe97fs
- Coding
- c.291del
- MANE Select
- NM_013436
- Type
- Deletion
- Location
- chr2:183003254 (GRCh38)
- Gene constraint
- LOEUF 0.14 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 92.75 · 5 PDB
- Residue 97
- an α-helix
Similar variants
- NCKAP1 c.3180+2del Likely pathogenic ★ same type
- NCKAP1 p.Ala1040fs Pathogenic ★ same type
- NCKAP1 p.Asn1080fs Pathogenic ★ same type
- NCKAP1 p.Asn52fs Likely pathogenic ★ same type
- NCKAP1 p.Gln228fs Likely pathogenic ★ same type
- NCKAP1 p.Lys1056_Leu1059del Likely pathogenic ★ same type
- NCKAP1 p.Lys501fs Likely pathogenic ★ same type
- NCKAP1 p.Met212fs Likely 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/nckap1-p-phe97fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown