ELP1 p.Asp460=
c.1380C>T · rs908952171 · VCV2809459
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 6.84e-05%)
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 0.78 | GERP -1.4, phastCons 0.85 |
| Overall | ||
| CADD | 2.241 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,722 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.Asp460=
- Coding
- c.1380C>T
- MANE Select
- NM_003640
- dbSNP
- rs908952171
- Type
- single nucleotide variant
- Location
- chr9:108908385 (GRCh38)
- Gene constraint
- LOEUF 0.803 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.31 · 5 PDB
Similar variants
- 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
- ELP1 c.2204+6T>C 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-asp460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown