NM_006118.4(HAX1):c.96TGA[2] (p.Asp34del) AND Kostmann syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 19, 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:: RCV000653740.4

Allele description [Variation Report for NM_006118.4(HAX1):c.96TGA[2] (p.Asp34del)]

NM_006118.4(HAX1):c.96TGA[2] (p.Asp34del)

Gene:

HAX1:HCLS1 associated protein X-1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_006118.4(HAX1):c.96TGA[2] (p.Asp34del)

HGVS:

NC_000001.11:g.154273378TGA[2]
NG_007369.1:g.5816TGA[2]
NM_001018837.2:c.54-104GAT[2]
NM_006118.4:c.96TGA[2]MANE SELECT
NP_006109.2:p.Asp34del
LRG_64t1:c.102_104del
LRG_64:g.5816TGA[2]
NC_000001.10:g.154245852_154245854del
NC_000001.10:g.154245854TGA[2]
NM_006118.3:c.102_104del
NM_006118.3:c.102_104delTGA

Protein change:

D34del

Links:

dbSNP: rs560912060

NCBI 1000 Genomes Browser:

rs560912060

Molecular consequence:

NM_006118.4:c.96TGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001018837.2:c.54-104GAT[2] - intron variant - [Sequence Ontology: SO:0001627]

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

Recent activity

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Bacteriophage P22 packaging genes
Bacteriophage P22 packaging genes
gi|215302|gb|M59749.1|P22PACK

Nucleotide
Poeciliopsis prolifica strain line A6 SCAFFOLD068, whole genome shotgun sequence
Poeciliopsis prolifica strain line A6 SCAFFOLD068, whole genome shotgun sequence
gi|2417705540|gb|JAPDDK010000068.1| WGS:JAPDDK01|SCAFFOLD068

Nucleotide
PREDICTED: Homo sapiens Fc receptor like 2 (FCRL2), transcript variant X2, mRNA
PREDICTED: Homo sapiens Fc receptor like 2 (FCRL2), transcript variant X2, mRNA
gi|2462513513|ref|XM_054338695.1|

Nucleotide
PREDICTED: Homo sapiens Fc receptor like 2 (FCRL2), transcript variant X7, mRNA
PREDICTED: Homo sapiens Fc receptor like 2 (FCRL2), transcript variant X7, mRNA
gi|2462513523|ref|XM_054338700.1|

Nucleotide
SRP117950 (16)
SRA

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000775630	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 19, 2022)	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

SCV000775630

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 19, 2022)

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, SCV000775630.3

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

Description

This variant, c.102_104del, results in the deletion of 1 amino acid(s) of the HAX1 protein (p.Asp34del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs560912060, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with HAX1-related conditions. ClinVar contains an entry for this variant (Variation ID: 543081). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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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