ELMOD2 p.Gln126=
c.378G>A · rs764726417 · VCV3033975
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00348%, amr)
Conditions
1
ELMOD2-related disorder
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 0.012 | GERP -3.8, phastCons 0.088 |
| Overall | ||
| CADD | 2.633 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00348%
Admixed American · 2/57,400 alleles
Filtering AF
0.000578%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000216%
Overall
0.000207%
3/1,445,906 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00348% | 28,700 |
| European (non-Finnish) | 8.52e-05% | 1,173,902 |
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
- ELMOD2
- Protein
- p.Gln126=
- Coding
- c.378G>A
- MANE Select
- NM_153702
- dbSNP
- rs764726417
- Type
- single nucleotide variant
- Location
- chr4:140537520 (GRCh38)
- Gene constraint
- LOEUF 0.881 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.39
- Residue 126
- the elmo domain
Disease context
ELMOD2-related disorder
Similar variants
- ELMOD2 p.Gly234Asp Uncertain significance ★ ⚠ same condition
- ELMOD2 p.Ser221Asn Likely benign same condition
- ELMOD2 c.142+43G>T Benign ★★ same type
- ELMOD2 c.270-81T>G Benign ★★ same type
- ELMOD2 c.-9-294A>G Benign ★★ same type
- ELMOD2 c.*9C>T Benign/Likely benign ★★ same type
- ELMOD2 p.Lys143Thr Benign/Likely benign ★★ same type
- ELMOD2 p.Val39Gly Likely benign ★★ 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/elmod2-p-gln126 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown