ELMOD3 p.Ala343=
c.1029C>A · rs116056110 · VCV787770
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.43%, 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 0.54 | GERP 1.3, phastCons 0.99 |
| Overall | ||
| CADD | 10.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.43%
African / African-American · 2,507/73,176 alleles
Filtering AF
3.31%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.27%
Overall
0.178%
2,764/1,551,676 alleles · low-frequency
exomes 1,365/1,399,344 · genomes 1,399/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.43% | 29 |
| Remaining individualsnot grpmax-eligible | 0.211% | 473 |
| Admixed American | 0.19% | 526 |
| Middle Eastern | 0.117% | 856 |
| South Asian | 0.00476% | 21,014 |
| European (non-Finnish) | 0.00192% | 52,137 |
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.Ala343=
- Coding
- c.1029C>A
- MANE Select
- NM_001135022
- dbSNP
- rs116056110
- Type
- single nucleotide variant
- Location
- chr2:85390845 (GRCh38)
- Gene constraint
- LOEUF 1.021 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.18
Similar variants
- 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
- 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-ala343 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown