ELMOD3 p.His243=
c.729C>T · rs202113724 · VCV2840615
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00445%, sas)
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 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 8.623 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00445%
South Asian · 4/89,860 alleles
Filtering AF
0.00144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0009%
Overall
0.000311%
5/1,607,458 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00445% | 22,465 |
| East Asian | 0.00225% | 44,402 |
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.His243=
- Coding
- c.729C>T
- MANE Select
- NM_001135022
- dbSNP
- rs202113724
- Type
- single nucleotide variant
- Location
- chr2:85377465 (GRCh38)
- Gene constraint
- LOEUF 1.021 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.18
- Residue 243
- the elmo domain
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-his243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown