ELN p.Gln638=
c.1914G>A · rs782650847 · VCV516591
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00274%, 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 0.59 | GERP 1.6, phastCons 0.99 |
| Overall | ||
| CADD | 5.414 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00274%
African / African-American · 2/73,072 alleles
Filtering AF
0.000454%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00017%
Overall
0.000194%
3/1,546,720 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00274% | 36,536 |
| European (non-Finnish) | 8.71e-05% | 1,147,533 |
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
- ELN
- Protein
- p.Gln638=
- Coding
- c.1914G>A
- MANE Select
- NM_000501
- dbSNP
- rs782650847
- Type
- single nucleotide variant
- Location
- chr7:74063365 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.20
- Residue 638
- the 'disordered' region
Similar variants
- ELN c.134-1G>A Likely pathogenic ★★ same type
- ELN c.377-2A>G Pathogenic/Likely pathogenic ★★ same type
- ELN c.643+1G>A Pathogenic/Likely pathogenic ★★ same type
- ELN c.643+1G>C Likely pathogenic ★★ same type
- ELN c.686-2A>G Likely pathogenic ★★ same type
- ELN c.800-1G>A Pathogenic/Likely pathogenic ★★ same type
- ELN c.800-2A>G Pathogenic ★★ same type
- ELN c.800-3C>G 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/eln-p-gln638 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown