ELMOD3 p.Ala234=
c.702G>A · rs371072018 · VCV2887932
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -1.2 | GERP -4.7 |
| Overall | ||
| CADD | 9.477 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,072 alleles
Filtering AF
0.0144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0137%
Overall
0.0131%
211/1,609,368 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,072 |
| European (non-Finnish) | 0.0163% | 6,135 |
| South Asian | 0.00887% | 11,274 |
| Remaining individualsnot grpmax-eligible | 0.00642% | 15,580 |
| African / African-American | 0.00402% | 24,873 |
| Admixed American | 0.00336% | 29,727 |
| East Asian | 0.00225% | 44,438 |
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.Ala234=
- Coding
- c.702G>A
- MANE Select
- NM_001135022
- dbSNP
- rs371072018
- Type
- single nucleotide variant
- Location
- chr2:85377438 (GRCh38)
- Gene constraint
- LOEUF 1.021 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.18
- Residue 234
- the elmo domain
Similar variants
- ELMOD3 p.Ala234Val Uncertain significance ★★ ⚠ same residue
- 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.His294Tyr Uncertain significance ★★ ⚠ same type
- ELMOD3 p.His297Tyr Uncertain significance ★★ ⚠ same type
- ELMOD3 p.Leu164Met 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-ala234 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown