NAF1 p.Pro79=
c.237G>A · VCV3667933
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0255%, afr)
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 -2.1 | GERP -2.7 |
| Overall | ||
| CADD | 2.952 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0255%
African / African-American · 19/74,532 alleles
Filtering AF
0.0167%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0138%
Overall
0.00163%
26/1,598,448 alleles · ultra-rare
exomes 11/1,446,424 · genomes 15/152,024 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0255% | 3,923 |
| Remaining individualsnot grpmax-eligible | 0.00811% | 12,324 |
| Admixed American | 0.00172% | 58,144 |
| European (non-Finnish) | 8.53e-05% | 1,172,586 |
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
- NAF1
- Protein
- p.Pro79=
- Coding
- c.237G>A
- MANE Select
- NM_138386
- Type
- single nucleotide variant
- Location
- chr4:163166491 (GRCh38)
- Structure
- AlphaFold pLDDT 72.47 · 8 PDB
- Residue 79
- the 'disordered' region
Similar variants
- NAF1 p.Pro79Ala Uncertain significance ★ ⚠ same residue
- NAF1 p.Pro79Leu Uncertain significance ★ ⚠ same residue
- NAF1 p.Ala102Ser Uncertain significance ★★ ⚠ same type
- NAF1 p.Ala323Val Uncertain significance ★★ ⚠ same type
- NAF1 p.Ala87Val Uncertain significance ★★ ⚠ same type
- NAF1 p.Arg106Trp Uncertain significance ★★ ⚠ same type
- NAF1 p.Arg437Cys Uncertain significance ★★ ⚠ same type
- NAF1 p.Arg437His 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/naf1-p-pro79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown