NEXMIF p.Phe207=
c.621C>T · rs755897828 · VCV2798608
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00217%, amr)
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 2.3 | GERP -0.83, phastCons 1 |
| Overall | ||
| CADD | 6.164 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00217%
Admixed American · 1/46,008 alleles
Overall
0.000165%
2/1,210,890 alleles · very rare
exomes 2/1,097,603 · genomes 0/113,287 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00217% | 46,008 |
| European (non-Finnish) | 0.000112% | 894,951 |
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
- NEXMIF
- Protein
- p.Phe207=
- Coding
- c.621C>T
- MANE Select
- NM_001008537
- dbSNP
- rs755897828
- Type
- single nucleotide variant
- Location
- chrX:74743936 (GRCh38)
- Structure
- AlphaFold pLDDT 40.87
- Residue 207
- a UniProt-annotated variant site (in xlid98; de novo dominant mutation found in females; disease phenotype includes epilepsy as a feature)
Similar variants
- NEXMIF p.Phe207Tyr Uncertain significance ★ ⚠ same residue
- NEXMIF p.Phe207fs Pathogenic ★★ same residue
- NEXMIF p.Arg218Ter Pathogenic ★★ same type
- NEXMIF p.Arg313Ter Pathogenic ★★ same type
- NEXMIF p.Arg322Ter Pathogenic ★★ same type
- NEXMIF p.Arg348Ter Pathogenic ★★ same type
- NEXMIF p.Arg481Ter Pathogenic ★★ same type
- NEXMIF p.Arg628Ter Pathogenic ★★ 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/nexmif-p-phe207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown