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NM_006118.4(HAX1):c.159T>A (p.Ser53Arg) AND Kostmann syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 31, 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:
RCV002815377.2

Allele description [Variation Report for NM_006118.4(HAX1):c.159T>A (p.Ser53Arg)]

NM_006118.4(HAX1):c.159T>A (p.Ser53Arg)

Gene:
HAX1:HCLS1 associated protein X-1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q21.3
Genomic location:
Preferred name:
NM_006118.4(HAX1):c.159T>A (p.Ser53Arg)
HGVS:
  • NC_000001.11:g.154273441T>A
  • NG_007369.1:g.5879T>A
  • NM_001018837.2:c.54-39T>A
  • NM_006118.4:c.159T>AMANE SELECT
  • NP_006109.2:p.Ser53Arg
  • NP_006109.2:p.Ser53Arg
  • LRG_64t1:c.159T>A
  • LRG_64:g.5879T>A
  • LRG_64p1:p.Ser53Arg
  • NC_000001.10:g.154245917T>A
  • NM_006118.3:c.159T>A
Protein change:
S53R
Molecular consequence:
  • NM_001018837.2:c.54-39T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006118.4:c.159T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Kostmann syndrome (SCN3)
Synonyms:
Kostmann disease; Agranulocytosis infantile; Autosomal recessive severe congenital neutropenia type 3
Identifiers:
MONDO: MONDO:0012548; MedGen: C5235141; Orphanet: 99749; OMIM: 610738

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003205447Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 31, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003205447.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 53 of the HAX1 protein (p.Ser53Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with HAX1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024