EHD3 p.Arg215=
c.645A>G · rs112609329 · VCV790500
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.82%, 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 -0.77 | GERP -5.2 |
| Overall | ||
| CADD | 6.336 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.82%
African / African-American · 1,369/75,038 alleles
Filtering AF
1.74%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.71%
Overall
0.104%
1,684/1,614,176 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.82% | 55 |
| Admixed American | 0.28% | 357 |
| Remaining individualsnot grpmax-eligible | 0.158% | 631 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.00549% | 18,218 |
| European (non-Finnish) | 0.00314% | 31,893 |
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
- EHD3
- Protein
- p.Arg215=
- Coding
- c.645A>G
- MANE Select
- NM_014600
- dbSNP
- rs112609329
- Type
- single nucleotide variant
- Location
- chr2:31260652 (GRCh38)
- Gene constraint
- LOEUF 0.578 · pLI 0.61 (gnomAD)
- Structure
- AlphaFold pLDDT 88.56
- Residue 215
- the dynamin-type g domain
Similar variants
- EHD3 c.502+9C>T Benign ★★ same type
- EHD3 p.Ala127Thr Uncertain significance ★ ⚠ same type
- EHD3 p.Ala131Thr Uncertain significance ★ ⚠ same type
- EHD3 p.Ala290Val Uncertain significance ★ ⚠ same type
- EHD3 p.Ala413Ser Uncertain significance ★ ⚠ same type
- EHD3 p.Ala437Thr Uncertain significance ★ ⚠ same type
- EHD3 p.Ala99Val Uncertain significance ★ ⚠ same type
- EHD3 p.Arg12Gly 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/ehd3-p-arg215 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown