ELP2 p.Ser714=
c.2142C>T · rs1598839021 · VCV721352
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, eas)
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 0.2 | GERP 0.58, phastCons 0.97 |
| Overall | ||
| CADD | 10.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,854 alleles
Filtering AF
0.00884%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.000496%
8/1,614,068 alleles · ultra-rare
exomes 8/1,461,880 · genomes 0/152,188 · joint denominator
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
- ELP2
- Protein
- p.Ser714=
- Coding
- c.2142C>T
- MANE Select
- NM_018255
- dbSNP
- rs1598839021
- Type
- single nucleotide variant
- Location
- chr18:36170128 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49 · 4 PDB
Similar variants
- ELP2 p.Arg140Ter Pathogenic/Likely pathogenic ★★ same type
- ELP2 p.Arg462Gln Pathogenic/Likely pathogenic ★★ same type
- ELP2 p.Gln192Ter Pathogenic/Likely pathogenic ★★ same type
- ELP2 p.His206Arg Pathogenic/Likely pathogenic ★★ same type
- ELP2 c.523+574G>A Uncertain significance ★★ same type
- ELP2 p.Ala741Val Uncertain significance ★★ ⚠ same type
- ELP2 p.Arg468Trp Uncertain significance ★★ ⚠ same type
- ELP2 p.Asp71Gly 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/elp2-p-ser714 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown