ELP1 p.Pro592=
c.1776A>G · rs774649863 · VCV1906094
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, 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 -6.3 | GERP -3.3 |
| Overall | ||
| CADD | 3.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,078 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000372%
6/1,613,998 alleles · very rare
exomes 6/1,461,702 · genomes 0/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,078 |
| European (non-Finnish) | 0.000424% | 235,980 |
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.Pro592=
- Coding
- c.1776A>G
- MANE Select
- NM_003640
- dbSNP
- rs774649863
- Type
- single nucleotide variant
- Location
- chr9:108902917 (GRCh38)
- Gene constraint
- LOEUF 0.803 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.31 · 5 PDB
- Residue 592
- a β-strand
Similar variants
- ELP1 p.Pro592Leu Uncertain significance ★ ⚠ same residue
- ELP1 p.Pro592Ser Uncertain significance ★ ⚠ same residue
- ELP1 p.Pro592_Lys594delinsGln Uncertain significance ★★ 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
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-pro592 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown