EFHC1 p.Phe398=
c.1194T>C · rs201946033 · VCV357483
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.337%, eas)
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 1.5 | GERP 0.6, phastCons 1 |
| Overall | ||
| CADD | 8.362 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.337%
East Asian · 151/44,866 alleles
Filtering AF
0.293%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.276%
Overall
0.00985%
159/1,614,090 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.337% | 297 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,417 |
| European (non-Finnish) | 0.000169% | 589,977 |
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
- EFHC1
- Protein
- p.Phe398=
- Coding
- c.1194T>C
- MANE Select
- NM_018100
- dbSNP
- rs201946033
- Type
- single nucleotide variant
- Location
- chr6:52469389 (GRCh38)
- Gene constraint
- LOEUF 0.906 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.31 · 2 PDB
Similar variants
- EFHC1 p.Ala445Thr Uncertain significance ★★ ⚠ same type
- EFHC1 p.Ala529Glu Uncertain significance ★★ ⚠ same type
- EFHC1 p.Ala590Pro Uncertain significance ★★ ⚠ same type
- EFHC1 p.Ala83Val Uncertain significance ★★ ⚠ same type
- EFHC1 p.Ala88Val Uncertain significance ★★ ⚠ same type
- EFHC1 p.Arg118Cys Uncertain significance ★★ ⚠ same type
- EFHC1 p.Arg151Leu Uncertain significance ★★ ⚠ same type
- EFHC1 p.Arg159Gln 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/efhc1-p-phe398 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown