ERN2 p.Gln620Ter
c.1858C>T · rs2506749148 · VCV2289592
Uncertain significance
Single submitter
Classification
Uncertain significance
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 |
|---|---|---|
| NMD | predicted | premature termination codon in exon 16 of 22 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.26 | loss · gain 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 43.0 | 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
- ERN2
- Protein
- p.Gln620Ter
- Coding
- c.1858C>T
- MANE Select
- NM_033266
- dbSNP
- rs2506749148
- Type
- single nucleotide variant
- Location
- chr16:23695061 (GRCh38)
- Gene constraint
- LOEUF 1.209 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.91 · 2 PDB
- Residue 620
- the protein kinase domain
Similar variants
- ERN2 p.Arg868Ter Uncertain significance ★★ same type
- ERN2 p.Val69Ile Benign ★★ ⚠ same type
- ERN2 p.Ala22Val Uncertain significance ★ ⚠ same type
- ERN2 p.Ala318Asp Uncertain significance ★ ⚠ same type
- ERN2 p.Ala395Val Uncertain significance ★ ⚠ same type
- ERN2 p.Ala4Thr Uncertain significance ★ ⚠ same type
- ERN2 p.Ala760Thr Uncertain significance ★ ⚠ same type
- ERN2 p.Ala80Thr 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/ern2-p-gln620ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown