NAF1 p.Phe241=
c.723C>T · rs780245066 · VCV2902544
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0054%, 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 4.5 | GERP 0.26, phastCons 1 |
| Overall | ||
| CADD | 13.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0054%
African / African-American · 4/74,044 alleles
Filtering AF
0.00176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00105%
Overall
0.000875%
14/1,599,858 alleles · very rare
exomes 12/1,447,920 · genomes 2/151,938 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0054% | 18,511 |
| Remaining individualsnot grpmax-eligible | 0.00484% | 20,661 |
| East Asian | 0.00451% | 22,179 |
| European (non-Finnish) | 0.000426% | 235,007 |
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.Phe241=
- Coding
- c.723C>T
- MANE Select
- NM_138386
- dbSNP
- rs780245066
- Type
- single nucleotide variant
- Location
- chr4:163140378 (GRCh38)
- Structure
- AlphaFold pLDDT 72.47 · 8 PDB
- Residue 241
- the 'interaction with nef' region
Similar variants
- NAF1 p.Phe241Leu 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
- NAF1 p.Asn17Ser 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-phe241 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown