EDAR p.Val336=
c.1008G>C · VCV4956412
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, nfe)
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 0.011 | GERP -1, phastCons 0.8 |
| Overall | ||
| CADD | 4.512 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
European (non-Finnish) · 26/1,180,034 alleles
Filtering AF
0.00153%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0013%
Overall
0.00185%
27/1,461,886 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0022% | 45,386 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
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
- EDAR
- Protein
- p.Val336=
- Coding
- c.1008G>C
- MANE Select
- NM_022336
- Type
- single nucleotide variant
- Location
- chr2:108906324 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.01 · 1 PDB
Similar variants
- EDAR p.Val336Met Uncertain significance ★★ ⚠ same residue
- EDAR p.Val336Glu Uncertain significance ★ ⚠ same residue
- EDAR c.730+1G>T Pathogenic ★★ same type
- EDAR p.Ala26Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- EDAR p.Arg25Ter Pathogenic/Likely pathogenic ★★ same type
- EDAR p.Arg358Ter Pathogenic ★★ same type
- EDAR p.Arg420Gln Pathogenic/Likely pathogenic ★★ same type
- EDAR p.Arg89His Pathogenic/Likely 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/edar-p-val336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown