ELMO2 p.Pro29=
c.87C>G · rs147152999 · VCV747850
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0758%, 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 0.063 | GERP -4.4, phastCons 0.49 |
| Overall | ||
| CADD | 8.197 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0758%
European (non-Finnish) · 894/1,179,908 alleles
Filtering AF
0.0716%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.07%
Overall
0.0617%
995/1,613,796 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0758% | 1,320 |
| Finnishnot grpmax-eligible | 0.0687% | 1,455 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,231 |
| Admixed American | 0.04% | 2,499 |
| Middle Eastern | 0.0164% | 6,084 |
| African / African-American | 0.00534% | 18,722 |
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.Pro29=
- Coding
- c.87C>G
- MANE Select
- NM_133171
- dbSNP
- rs147152999
- Type
- single nucleotide variant
- Location
- chr20:46394081 (GRCh38)
- Gene constraint
- LOEUF 0.486 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 88.96 · 2 PDB
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-pro29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown