ELANE p.Met1Thr
c.2T>C · rs2035606369 · VCV988327
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
start-loss
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 | start-loss | predicted loss-of-function |
|---|---|---|
| REVEL | 0.69 | pathogenic-leaning |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 18.76 | 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
- ELANE
- Protein
- p.Met1Thr
- Coding
- c.2T>C
- MANE Select
- NM_001972
- dbSNP
- rs2035606369
- Type
- single nucleotide variant
- Location
- chr19:852330 (GRCh38)
- Gene constraint
- LOEUF 1.245 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.42 · 38 PDB
Similar variants
- ELANE p.Met1Ile Pathogenic/Likely pathogenic ★★ same residue
- ELANE p.Met1Val Pathogenic ★★ same residue
- ELANE p.Met1Leu Likely pathogenic same residue
- ELANE c.597+1G>A Pathogenic ★★ same type
- ELANE c.597+1G>C Pathogenic ★★ same type
- ELANE c.597+1G>T Pathogenic ★★ same type
- ELANE c.597+5G>A Pathogenic/Likely pathogenic ★★ same type
- ELANE p.Ala57Thr Pathogenic/Likely 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/elane-p-met1thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown