ELMOD3 p.His294=
c.882C>T · rs17850708 · VCV508141
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 7.08%, nfe) — too common for a highly-penetrant pathogenic allele
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 0.55 | GERP -1.1, phastCons 0.93 |
| Overall | ||
| CADD | 6.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.08%
European (non-Finnish) · 83,542/1,179,994 alleles
Filtering AF
7.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.02%
Overall
6.24%
100,714/1,614,146 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 7.08% | 14 |
| South Asian | 6.03% | 17 |
| Remaining individualsnot grpmax-eligible | 5.59% | 18 |
| African / African-American | 4.64% | 22 |
| Amishnot grpmax-eligible | 4.39% | 23 |
| Admixed American | 3.27% | 31 |
| Middle Eastern | 2.97% | 34 |
| Ashkenazi Jewishnot grpmax-eligible | 2.1% | 48 |
| Finnishnot grpmax-eligible | 2.04% | 49 |
| East Asian | 1.33% | 75 |
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
- ELMOD3
- Protein
- p.His294=
- Coding
- c.882C>T
- MANE Select
- NM_001135022
- dbSNP
- rs17850708
- Type
- single nucleotide variant
- Location
- chr2:85390204 (GRCh38)
- Gene constraint
- LOEUF 1.021 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.18
- Residue 294
- the elmo domain
Similar variants
- ELMOD3 p.His294Tyr Uncertain significance ★★ ⚠ same residue
- ELMOD3 p.His294Arg Uncertain significance ★ ⚠ same residue
- ELMOD3 p.Ala234Val Uncertain significance ★★ ⚠ same type
- ELMOD3 p.Ala289Val Uncertain significance ★★ ⚠ same type
- ELMOD3 p.Ala38Thr Uncertain significance ★★ ⚠ same type
- ELMOD3 p.Gln100Ter Uncertain significance ★★ same type
- ELMOD3 p.Gln371Ter Uncertain significance ★★ same type
- ELMOD3 p.His297Tyr 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/elmod3-p-his294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown