ELMOD2 p.Asp88=
c.264T>C · VCV4968674
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.023%, 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 -2.1 | GERP -2.6 |
| Overall | ||
| CADD | 8.567 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.023%
African / African-American · 17/73,818 alleles
Filtering AF
0.0146%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.012%
Overall
0.00119%
19/1,599,042 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.023% | 4,342 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,952 |
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.Asp88=
- Coding
- c.264T>C
- MANE Select
- NM_153702
- Type
- single nucleotide variant
- Location
- chr4:140535825 (GRCh38)
- Gene constraint
- LOEUF 0.881 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.39
Similar variants
- ELMOD2 p.Asp88Glu Uncertain significance ★ ⚠ same residue
- 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
- ELMOD2 p.Arg167Ser 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/elmod2-p-asp88 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown