NM_006118.4(HAX1):c.107AAG[4] (p.Glu40del) AND Kostmann syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 27, 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:: RCV000889401.11

Allele description [Variation Report for NM_006118.4(HAX1):c.107AAG[4] (p.Glu40del)]

NM_006118.4(HAX1):c.107AAG[4] (p.Glu40del)

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.107AAG[4] (p.Glu40del)

HGVS:

NC_000001.11:g.154273389AAG[4]
NG_007369.1:g.5827AAG[4]
NM_001018837.2:c.54-92GAA[4]
NM_006118.4:c.107AAG[4]MANE SELECT
NP_006109.2:p.Glu40del
LRG_64t1:c.119_121del
LRG_64:g.5827AAG[4]
NC_000001.10:g.154245864_154245866del
NC_000001.10:g.154245865AAG[4]
NM_006118.3:c.119_121del
NM_006118.3:c.119_121delAAG

Protein change:

E40del

Links:

dbSNP: rs753894148

NCBI 1000 Genomes Browser:

rs753894148

Molecular consequence:

NM_006118.4:c.107AAG[4] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001018837.2:c.54-92GAA[4] - 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

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001033080	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 27, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001461734	Natera, Inc.	no assertion criteria provided	Likely benign (Sep 16, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001033080

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 27, 2024)

germline

clinical testing

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

SCV001461734

Natera, Inc.

no assertion criteria provided

Likely benign
(Sep 16, 2020)

germline

clinical testing

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, SCV001033080.6

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

#	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

From Natera, Inc., SCV001461734.1

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

#	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

ClinVar

Relating variation to medicine