Is ELANE p.Val101Met (c.301G>A) pathogenic?

ELANE p.Val101Met (c.301G>A) is classified Pathogenic in ELANE (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-08-17). AlphaMissense: likely pathogenic (0.651); Absent from gnomAD v4.1; Associated with cyclic neutropenia.

What condition is associated with ELANE p.Val101Met (c.301G>A)?

ELANE p.Val101Met (c.301G>A) is associated with cyclic neutropenia, neutropenia, severe congenital, 1, autosomal dominant (ClinVar).

How common is ELANE p.Val101Met (c.301G>A) in the general population?

ELANE p.Val101Met (c.301G>A) is absent from gnomAD v4.1 (gnomAD).

How is Cyclic neutropenia inherited?

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

What do computational predictors say about ELANE p.Val101Met (c.301G>A)?

AlphaMissense predicts likely pathogenic (score 0.651) — an in-silico prediction, not a clinical call.

ELANE p.Val101Met

c.301G>A · rs137854449 · VCV844491

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.651 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,611,138)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

cyclic neutropenia

Computational evidence

Protein change
AlphaMissense	0.651	likely pathogenic ✓ concordant with ClinVar
REVEL	0.596	indeterminate
SaProt	LLR -13.86	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.2	GERP -4.5
Regional constraint	o/e 1.04	unconstrained · MANE · 3,171 bp · p 0.52 · regional, not allelic
Overall
CADD	13.16	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

No allele count reported in gnomAD v4.1 (AN 1,611,138). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ELANE
Protein: p.Val101Met
Coding: c.301G>A
MANE Select: NM_001972
dbSNP: rs137854449
Type: single nucleotide variant
Location: chr19:853338 (GRCh38)
Gene constraint: LOEUF 1.245 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.42 · 38 PDB
Residue 101: a β-strand; the peptidase s1 domain; a UniProt-annotated variant site (in scn1; located on the same allele as l-98; reduces proteolytic enzyme activity by slightly less than half; together with l-98 shows an additive effect with minimal remaining enzyme activity); a UniProt-annotated variant site (in scn1)

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: 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.Val101Gly Pathogenic same residue
ELANE p.Val101fs Uncertain significance ★★ same residue
ELANE p.Val101= Benign/Likely benign ★★ 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

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-val101met (accessed [today's date]).

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