EFHC2 p.Phe320=
c.960C>T · rs372092672 · VCV2660365
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0141%, 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 0.41 | GERP -1.1, phastCons 0.99 |
| Overall | ||
| CADD | 2.744 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0141%
African / African-American · 8/56,918 alleles
Filtering AF
0.00692%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00612%
Overall
0.00747%
90/1,204,477 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0141% | 7,115 |
| Remaining individualsnot grpmax-eligible | 0.0127% | 7,902 |
| European (non-Finnish) | 0.00819% | 12,209 |
| South Asian | 0.00533% | 18,766 |
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
- EFHC2
- Protein
- p.Phe320=
- Coding
- c.960C>T
- MANE Select
- NM_025184
- dbSNP
- rs372092672
- Type
- single nucleotide variant
- Location
- chrX:44248815 (GRCh38)
- Structure
- AlphaFold pLDDT 79.83 · 4 PDB
- Residue 320
- the dm10 2 domain
Similar variants
- EFHC2 p.Glu506Lys Likely benign ★★ ⚠ same type
- EFHC2 p.Glu507Gln Benign ★★ ⚠ same type
- EFHC2 p.Ala549Gly Uncertain significance ★ ⚠ same type
- EFHC2 p.Ala697Ser Uncertain significance ★ ⚠ same type
- EFHC2 p.Arg133His Uncertain significance ★ ⚠ same type
- EFHC2 p.Arg135Gln Conflicting classifications of pathogenicity ★ ⚠ same type
- EFHC2 p.Arg135Trp Uncertain significance ★ ⚠ same type
- EFHC2 p.Arg163Gln 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/efhc2-p-phe320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown