NCF4 p.Lys253=
c.759G>A · VCV4947716
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.112 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor loss · deltas |
| Constraint at this position | ||
| Conservation | phyloP 4.2 | GERP -0.87, phastCons 1 |
| Overall | ||
| CADD | 12.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- NCF4
- Protein
- p.Lys253=
- Coding
- c.759G>A
- MANE Select
- NM_000631
- Type
- single nucleotide variant
- Location
- chr22:36876029 (GRCh38)
- Gene constraint
- LOEUF 1.005 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 84.48 · 6 PDB
- Residue 253
- the pb1 domain; a β-strand
Similar variants
- NCF4 c.118-1G>A Pathogenic/Likely pathogenic ★★ same type
- NCF4 c.759-40C>T Pathogenic ★★ same type
- NCF4 p.Arg105Gln Pathogenic ★★ same type
- NCF4 c.758+24C>T Uncertain significance ★★ same type
- NCF4 c.758+32G>A Uncertain significance ★★ same type
- NCF4 c.758+39T>A Uncertain significance ★★ same type
- NCF4 c.758+51G>A Uncertain significance ★★ same type
- NCF4 c.758+62C>T 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/ncf4-p-lys253 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown