NM_001972.4(ELANE):c.242G>C (p.Arg81Pro) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 26, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003772372.1

Allele description

NM_001972.4(ELANE):c.242G>C (p.Arg81Pro)

Gene:

ELANE:elastase, neutrophil expressed [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_001972.4(ELANE):c.242G>C (p.Arg81Pro)

HGVS:

NC_000019.10:g.853279G>C
NG_009627.1:g.5989G>C
NM_001972.4:c.242G>CMANE SELECT
NP_001963.1:p.Arg81Pro
LRG_57:g.5989G>C
NC_000019.9:g.853279G>C

Protein change:

R81P

Links:

dbSNP: rs762470485

NCBI 1000 Genomes Browser:

rs762470485

Molecular consequence:

NM_001972.4:c.242G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cyclical neutropenia
Synonyms:: Cyclic hematopoiesis
Identifiers:: MONDO: MONDO:0008090; MedGen: C0221023; Orphanet: 2686; OMIM: 162800; Human Phenotype Ontology: HP:0040289

Name:: Neutropenia, severe congenital, 1, autosomal dominant
Identifiers:: MONDO: MONDO:0042490; MedGen: C1859966; OMIM: 202700

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004571442	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 26, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 14962902, 25705433, 31965297, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004571442

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 26, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in the ELA2 gene correlate with more severe expression of neutropenia: a study of 81 patients from the French Neutropenia Register.

Bellanné-Chantelot C, Clauin S, Leblanc T, Cassinat B, Rodrigues-Lima F, Beaufils S, Vaury C, Barkaoui M, Fenneteau O, Maier-Redelsperger M, Chomienne C, Donadieu J.

Blood. 2004 Jun 1;103(11):4119-25. Epub 2004 Feb 12.

PubMed [citation]

PMID:: 14962902

Severe congenital neutropenia caused by the ELANE gene mutation in a Vietnamese boy with misdiagnosis of tuberculosis and autoimmune neutropenia: a case report.

Vu QV, Wada T, Tran TT, Ngo DN, Van Dinh T, Nguyen CH, Le HT, Yachie A, Nguyen SN.

BMC Hematol. 2015;15:2. doi: 10.1186/s12878-015-0020-x.

PubMed [citation]

PMID:: 25705433
PMCID:: PMC4335412

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004571442.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ELANE protein function. ClinVar contains an entry for this variant (Variation ID: 1343817). This variant is also known as c.2190G>C; R52P. This missense change has been observed in individual(s) with ELANE-related conditions (PMID: 14962902, 25705433, 31965297). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 81 of the ELANE protein (p.Arg81Pro).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 5, 2024

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