ELP1 p.Ser910=
c.2730A>G · rs1183324668 · VCV1625967
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 -0.26 | GERP -2.2, phastCons 0.5 |
| Overall | ||
| CADD | 6.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,008 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.00131%
2/152,178 alleles · very rare
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
- ELP1
- Protein
- p.Ser910=
- Coding
- c.2730A>G
- MANE Select
- NM_003640
- dbSNP
- rs1183324668
- Type
- single nucleotide variant
- Location
- chr9:108896502 (GRCh38)
- Gene constraint
- LOEUF 0.803 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.31 · 5 PDB
- Residue 910
- the 'mediates dimerization' region
Similar variants
- ELP1 p.Ser910Ter Pathogenic ★ same residue
- ELP1 c.1361-1G>T Pathogenic/Likely pathogenic ★★ same type
- ELP1 c.1361-2A>G Pathogenic/Likely pathogenic ★★ same type
- ELP1 c.1461-1G>A Likely pathogenic ★★ same type
- ELP1 c.1644-1G>T Likely pathogenic ★★ same type
- ELP1 c.1644-2A>C Likely pathogenic ★★ same type
- ELP1 c.1854+1G>A Likely pathogenic ★★ same type
- ELP1 c.2015-2A>G Likely pathogenic ★★ 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/elp1-p-ser910 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown