ELN p.Tyr677Ter
c.2031C>G · rs1554688700 · VCV451699
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 30 of 33 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -9.5 | GERP -6.2 |
| Overall | ||
| CADD | 32.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Tyr677Ter
- Coding
- c.2031C>G
- MANE Select
- NM_000501
- dbSNP
- rs1554688700
- Type
- single nucleotide variant
- Location
- chr7:74065731 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.20
- Residue 677
- a modified residue (4-hydroxyproline; partial)
Similar variants
- ELN p.Tyr677= Uncertain significance ★ 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-tyr677ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown