NM_001972.4(ELANE):c.269C>A (p.Ser90Ter) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 22, 2024
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:: RCV003787733.2

Allele description [Variation Report for NM_001972.4(ELANE):c.269C>A (p.Ser90Ter)]

NM_001972.4(ELANE):c.269C>A (p.Ser90Ter)

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.269C>A (p.Ser90Ter)

HGVS:

NC_000019.10:g.853306C>A
NG_009627.1:g.6016C>A
NM_001972.4:c.269C>AMANE SELECT
NP_001963.1:p.Ser90Ter
NP_001963.1:p.Ser90Ter
LRG_57t1:c.269C>A
LRG_57:g.6016C>A
LRG_57p1:p.Ser90Ter
NC_000019.9:g.853306C>A
NM_001972.2:c.269C>A

Protein change:

S90*

Molecular consequence:

NM_001972.4:c.269C>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004604227	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 22, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004604227

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 22, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004604227.1

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

Description

This sequence change creates a premature translational stop signal (p.Ser90*) in the ELANE gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in ELANE cause disease. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ELANE-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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