ELMOD3 p.Ala204=
c.612G>C · rs202233755 · VCV1318244
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.11%, eas)
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 -1.8 | GERP -4.7 |
| Overall | ||
| CADD | 1.429 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.11%
East Asian · 48/43,826 alleles
Filtering AF
0.0848%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0761%
Overall
0.00532%
85/1,597,158 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.11% | 913 |
| African / African-American | 0.0391% | 2,554 |
| Middle Eastern | 0.0167% | 5,986 |
| Admixed American | 0.0087% | 11,490 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,816 |
| European (non-Finnish) | 8.53e-05% | 1,172,222 |
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.Ala204=
- Coding
- c.612G>C
- MANE Select
- NM_001135022
- dbSNP
- rs202233755
- Type
- single nucleotide variant
- Location
- chr2:85377348 (GRCh38)
- Gene constraint
- LOEUF 1.021 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.18
- Residue 204
- the elmo domain
Similar variants
- ELMOD3 p.Ala204Val 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.His294Tyr 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-ala204 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown