ELN p.Val141Gly
c.422T>G · VCV4082635
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9339 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, SaProt · REVEL no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9339 | likely pathogenic · top 5% in ELN |
|---|---|---|
| REVEL | 0.543 | indeterminate |
| SaProt | LLR -9.55 | tolerated |
| ⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.27 | loss · gain 0.08 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 6.4, phastCons 1 |
| Regional constraint | o/e 0.91 | unconstrained · MANE · 41 kb · p 0.005 · regional, not allelic |
| Overall | ||
| CADD | 25.4 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ELN
- Protein
- p.Val141Gly
- Coding
- c.422T>G
- MANE Select
- NM_000501
- Type
- single nucleotide variant
- Location
- chr7:74043163 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.20
Similar variants
- ELN p.Val141fs Pathogenic ★ same residue
- 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
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-val141gly (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown