Is ELANE p.Gln97Pro (c.290A>C) pathogenic?

ELANE p.Gln97Pro (c.290A>C) is classified Likely pathogenic in ELANE (ClinVar, Single submitter, 1 submitter; last evaluated 2018-11-09). AlphaMissense: likely pathogenic (0.9794); Absent from gnomAD v4.1.

How common is ELANE p.Gln97Pro (c.290A>C) in the general population?

ELANE p.Gln97Pro (c.290A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ELANE p.Gln97Pro (c.290A>C)?

AlphaMissense predicts likely pathogenic (score 0.9794) — an in-silico prediction, not a clinical call.

ELANE p.Gln97Pro

c.290A>C · rs1085307717 · VCV426627

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9794 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9794	likely pathogenic ✓ concordant with ClinVar · top 5% in ELANE
REVEL	0.831	moderately pathogenic-leaning
SaProt	LLR -18.18	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.3, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 3,171 bp · p 0.52 · regional, not allelic
Overall
CADD	23.4	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: ELANE
Protein: p.Gln97Pro
Coding: c.290A>C
MANE Select: NM_001972
dbSNP: rs1085307717
Type: single nucleotide variant
Location: chr19:853327 (GRCh38)
Gene constraint: LOEUF 1.245 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.42 · 38 PDB
Residue 97: a β-strand; the peptidase s1 domain; a UniProt-annotated variant site (in ch)

Full ELANE gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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
ELANE p.Ala57Val Pathogenic/Likely pathogenic ★★ same type
ELANE p.Ala61Val Pathogenic/Likely pathogenic ★★ ⚠ same type
ELANE p.Arg103Leu 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-gln97pro (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown