ENAH p.Ser2=
c.6T>C · VCV3508422
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0175%, 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 0.87 | GERP -2, phastCons 0.97 |
| Overall | ||
| CADD | 11.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0175%
African / African-American · 13/74,186 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0082%
Overall
0.000938%
15/1,599,740 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0175% | 5,707 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,989 |
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
- ENAH
- Protein
- p.Ser2=
- Coding
- c.6T>C
- MANE Select
- NM_018212
- Type
- single nucleotide variant
- Location
- chr1:225567414 (GRCh38)
- Gene constraint
- LOEUF 0.423 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.69 · 28 PDB
- Residue 2
- the wh1 domain
Similar variants
- ENAH p.Ser265Leu Likely benign ★★ same type
- ENAH c.1538+2899C>T Uncertain significance ★ ⚠ same type
- ENAH p.Ala393Val Uncertain significance ★ ⚠ same type
- ENAH p.Arg152Trp Uncertain significance ★ ⚠ same type
- ENAH p.Arg158Trp Uncertain significance ★ ⚠ same type
- ENAH p.Arg165Lys Uncertain significance ★ ⚠ same type
- ENAH p.Arg173Thr Uncertain significance ★ ⚠ same type
- ENAH p.Arg185Leu 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/enah-p-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown