Is ELANE p.Cys55Ser (c.164G>C) pathogenic?

ELANE p.Cys55Ser (c.164G>C) is classified Pathogenic in ELANE (ClinVar, Single submitter, 1 submitter; last evaluated 2015-02-09). AlphaMissense: likely pathogenic (0.9869); Absent from gnomAD v4.1.

How common is ELANE p.Cys55Ser (c.164G>C) in the general population?

ELANE p.Cys55Ser (c.164G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ELANE p.Cys55Ser (c.164G>C)?

AlphaMissense predicts likely pathogenic (score 0.9869) — an in-silico prediction, not a clinical call.

ELANE p.Cys55Ser

c.164G>C · rs2035617210 · VCV988289

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9869 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9869	likely pathogenic ✓ concordant with ClinVar · top 3% in ELANE
REVEL	0.902	moderately pathogenic-leaning
SaProt	LLR -11.54	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 9.2	GERP 2.4, phastCons 1
Regional constraint	o/e 0.31	constrained · MANE · 62 bp · p 0.00023 · regional, not allelic
Overall
CADD	24.6	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.Cys55Ser
Coding: c.164G>C
MANE Select: NM_001972
dbSNP: rs2035617210
Type: single nucleotide variant
Location: chr19:852972 (GRCh38)
Gene constraint: LOEUF 1.245 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.42 · 38 PDB
Residue 55: a disulfide bond; a β-strand; a UniProt-annotated variant site (in scn1); the peptidase s1 domain

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

Similar variants

ELANE p.Cys55= Likely benign ★★ same residue
ELANE p.Cys55Arg Likely pathogenic ★ same residue
ELANE p.Cys55Tyr Pathogenic ★ same residue
ELANE p.Cys55Ter Uncertain significance ★ same residue
ELANE p.Cys55del Uncertain significance ★ 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

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-cys55ser (accessed [today's date]).

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