Is ELANE p.Gly33= (c.99C>T) pathogenic?

ELANE p.Gly33= (c.99C>T) is classified Benign/Likely benign in ELANE (ClinVar, Multiple submitters, 12 submitters; last evaluated 2026-01-31). Low-frequency (popmax 1.38%, afr); Associated with cyclic neutropenia.

What condition is associated with ELANE p.Gly33= (c.99C>T)?

ELANE p.Gly33= (c.99C>T) is associated with cyclic neutropenia, autoinflammatory syndrome, neutropenia, severe congenital, 1, autosomal dominant (ClinVar).

How common is ELANE p.Gly33= (c.99C>T) in the general population?

ELANE p.Gly33= (c.99C>T) is low-frequency (popmax 1.38%, afr) (gnomAD).

How is Cyclic neutropenia inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

ELANE p.Gly33=

c.99C>T · rs17216628 · VCV258502

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.38%, afr)

Conditions

cyclic neutropenia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.72	GERP -3.7
Overall
CADD	8.517	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.38% African / African-American · 1,035/74,924 alleles

Filtering AF 1.31% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.28%

Overall 0.0743% 1,186/1,596,370 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.38%	72
Admixed American	0.166%	604
Remaining individualsnot grpmax-eligible	0.0645%	1,551
South Asian	0.00331%	30,246
European (non-Finnish)	0.000765%	130,801

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ELANE
Protein: p.Gly33=
Coding: c.99C>T
MANE Select: NM_001972
dbSNP: rs17216628
Type: single nucleotide variant
Location: chr19:852907 (GRCh38)
Gene constraint: LOEUF 1.245 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.42 · 38 PDB
Residue 33: the peptidase s1 domain

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

Disease context

cyclic neutropenia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autoinflammatory syndrome neutropenia, severe congenital, 1, autosomal dominant

For Cyclic neutropenia (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

ELANE p.Gly33fs Conflicting classifications of pathogenicity ★ same residue
ELANE p.Gly33Ser Uncertain significance ★★ ⚠ same residue
ELANE c.597+1G>A Pathogenic ★★ same condition
ELANE c.597+1G>C Pathogenic ★★ same condition
ELANE c.597+1G>T Pathogenic ★★ same condition
ELANE c.597+5G>A Pathogenic/Likely pathogenic ★★ same condition
ELANE p.Ala57Thr Pathogenic/Likely pathogenic ★★ same condition
ELANE p.Ala61Val Pathogenic/Likely pathogenic ★★ ⚠ same condition

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-gly33 (accessed [today's date]).

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