ELP4 p.Ala5=
c.15A>C · rs368443240 · VCV771804
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0587%, 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 -0.078 | GERP -3.9 |
| Overall | ||
| CADD | 6.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0587%
African / African-American · 44/74,942 alleles
Filtering AF
0.0449%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0401%
Overall
0.00328%
53/1,614,010 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0587% | 1,703 |
| Admixed American | 0.01% | 10,001 |
| European (non-Finnish) | 0.000254% | 393,348 |
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
- ELP4
- Protein
- p.Ala5=
- Coding
- c.15A>C
- MANE Select
- NM_019040
- dbSNP
- rs368443240
- Type
- single nucleotide variant
- Location
- chr11:31509799 (GRCh38)
- Gene constraint
- LOEUF 1.377 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.49
Similar variants
- PAX6 p.Arg222Trp Pathogenic/Likely pathogenic ★★ same type
- PAX6 p.Ter437Gln Pathogenic/Likely pathogenic ★★ same type
- PAX6 p.Ter437Leu Pathogenic/Likely pathogenic ★★ same type
- ELP4 p.Arg163His Uncertain significance ★★ ⚠ same type
- ELP4 p.Arg31Ser Uncertain significance ★★ ⚠ same type
- ELP4 p.Arg395His Uncertain significance ★★ ⚠ same type
- ELP4 p.Asn244Ser Uncertain significance ★★ ⚠ same type
- ELP4 p.Gln165Pro 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/elp4-p-ala5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown