NAF1 p.Ser142=
c.426T>G · rs145217718 · VCV2162126
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.109%, 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 -6.9 | GERP -3.1 |
| Overall | ||
| CADD | 0.192 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.109%
African / African-American · 81/74,516 alleles
Filtering AF
0.0895%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0825%
Overall
0.0146%
234/1,601,716 alleles · rare
exomes 184/1,449,392 · genomes 50/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.109% | 920 |
| Middle Eastern | 0.0331% | 3,022 |
| South Asian | 0.0297% | 3,370 |
| Admixed American | 0.0275% | 3,639 |
| Remaining individualsnot grpmax-eligible | 0.0177% | 5,638 |
| European (non-Finnish) | 0.00809% | 12,367 |
| East Asian | 0.0045% | 22,202 |
| Finnishnot grpmax-eligible | 0.00157% | 63,842 |
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.Ser142=
- Coding
- c.426T>G
- MANE Select
- NM_138386
- dbSNP
- rs145217718
- Type
- single nucleotide variant
- Location
- chr4:163164331 (GRCh38)
- Structure
- AlphaFold pLDDT 72.47 · 8 PDB
- Residue 142
- the 'disordered' region; the 'interaction with nef' region
Similar variants
- TNIP1 p.Ala142Thr Likely benign ★ 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-ser142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown