NEMF p.Asp359=
c.1077C>T · VCV4921660
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0573%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.5 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 10.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0573%
African / African-American · 43/75,016 alleles
Filtering AF
0.0437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.039%
Overall
0.00353%
57/1,614,114 alleles · ultra-rare
exomes 34/1,461,848 · genomes 23/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0573% | 1,745 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| Admixed American | 0.00666% | 15,006 |
| European (non-Finnish) | 0.000339% | 295,003 |
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
- NEMF
- Protein
- p.Asp359=
- Coding
- c.1077C>T
- MANE Select
- NM_004713
- Type
- single nucleotide variant
- Location
- chr14:49829209 (GRCh38)
- Gene constraint
- LOEUF 0.687 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.96 · 2 PDB
- Residue 359
- an α-helix
Similar variants
- NEMF p.Arg671Ter Pathogenic ★★ same type
- NEMF p.Tyr470Ter Pathogenic ★★ same type
- NEMF p.Arg934Ser Uncertain significance ★★ ⚠ same type
- NEMF p.Ile248Thr Uncertain significance ★★ ⚠ same type
- NEMF p.Pro584Ser Uncertain significance ★★ ⚠ same type
- NEMF p.Ser785Pro Uncertain significance ★★ ⚠ same type
- NEMF c.1915+8C>T Likely benign ★★ same type
- NEMF p.Ala75= Benign ★★ 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/nemf-p-asp359 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown