NEXMIF p.Pro77=
c.231G>A · rs757068776 · VCV1626558
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00878%, sas)
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 1.8 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 0.931 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00878%
South Asian · 5/56,946 alleles
Filtering AF
0.0034%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00216%
Overall
0.000826%
10/1,211,383 alleles · very rare
exomes 10/1,098,088 · genomes 0/113,295 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00878% | 11,389 |
| African / African-American | 0.00173% | 57,712 |
| European (non-Finnish) | 0.000447% | 223,851 |
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.Pro77=
- Coding
- c.231G>A
- MANE Select
- NM_001008537
- dbSNP
- rs757068776
- Type
- single nucleotide variant
- Location
- chrX:74744326 (GRCh38)
- Structure
- AlphaFold pLDDT 40.87
Similar variants
- NEXMIF p.Pro77Leu Uncertain significance ★ ⚠ 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
- NEXMIF p.Gln1137Ter 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-pro77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown