NEMF p.Val213=
c.639G>C · VCV3388713
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.021 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.27 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -0.31, phastCons 0.97 |
| Overall | ||
| CADD | 7.715 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,938 alleles
Filtering AF
0.000554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000262%
Overall
0.000809%
13/1,606,082 alleles · very rare
exomes 13/1,453,934 · genomes 0/152,148 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,969 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,278 |
| African / African-American | 0.00134% | 74,806 |
| European (non-Finnish) | 0.000767% | 130,314 |
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.Val213=
- Coding
- c.639G>C
- MANE Select
- NM_004713
- Type
- single nucleotide variant
- Location
- chr14:49834385 (GRCh38)
- Gene constraint
- LOEUF 0.687 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.96 · 2 PDB
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-val213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown