ELMO2 p.Gln422=
c.1266G>A · VCV4945229
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00314%, nfe)
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 3.1 | GERP 0.19, phastCons 1 |
| Overall | ||
| CADD | 12.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00314%
European (non-Finnish) · 37/1,179,966 alleles
Filtering AF
0.00231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00202%
Overall
0.00235%
38/1,613,916 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00314% | 31,891 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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
- ELMO2
- Protein
- p.Gln422=
- Coding
- c.1266G>A
- MANE Select
- NM_133171
- Type
- single nucleotide variant
- Location
- chr20:46374345 (GRCh38)
- Gene constraint
- LOEUF 0.486 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 88.96 · 2 PDB
- Residue 422
- the elmo domain; a turn
Similar variants
- ELMO2 p.Arg478Gln Uncertain significance ★★ ⚠ same type
- ELMO2 p.Asn490Lys Uncertain significance ★★ ⚠ same type
- ELMO2 p.Glu468Asp Uncertain significance ★★ ⚠ same type
- ELMO2 p.Ser396Gly Uncertain significance ★★ ⚠ same type
- ELMO2 p.Thr482Ala Uncertain significance ★★ ⚠ same type
- ELMO2 c.1065+87A>G Benign ★★ same type
- ELMO2 c.1066-47T>C Benign ★★ same type
- ELMO2 c.1580+23C>G 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/elmo2-p-gln422 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown