NC_000023.10:g.(?_135067662)_(136652229_?)del AND Hyper-IgM syndrome type 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 27, 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:: RCV001956451.7

Allele description [Variation Report for NC_000023.10:g.(?_135067662)_(136652229_?)del]

NC_000023.10:g.(?_135067662)_(136652229_?)del

Genes:

CD40LG:CD40 ligand [Gene - OMIM - HGNC]
GPR101:G protein-coupled receptor 101 [Gene - OMIM - HGNC]
HTATSF1:HIV-1 Tat specific factor 1 [Gene - OMIM - HGNC]
MAP7D3:MAP7 domain containing 3 [Gene - OMIM - HGNC]
RBMX:RNA binding motif protein X-linked [Gene - OMIM - HGNC]
ARHGEF6:Rac/Cdc42 guanine nucleotide exchange factor 6 [Gene - OMIM - HGNC]
ZIC3:Zic family member 3 [Gene - OMIM - HGNC]
ADGRG4:adhesion G protein-coupled receptor G4 [Gene - OMIM - HGNC]
BRS3:bombesin receptor subtype 3 [Gene - OMIM - HGNC]
FHL1:four and a half LIM domains 1 [Gene - OMIM - HGNC]
SLC9A6:solute carrier family 9 member A6 [Gene - OMIM - HGNC]
VGLL1:vestigial like family member 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq26.3

Genomic location:

ChrX: 135067662 - 136652229 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_135067662)_(136652229_?)del

HGVS:

NC_000023.10:g.(?_135067662)_(136652229_?)del

Condition(s)

Name:: Hyper-IgM syndrome type 1
Synonyms:: Immunodeficiency with hyper IgM type 1; Hyper IgM immunodeficiency, X-linked; Hyper-IgM Immunodeficiency Syndrome, Type 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010626; MedGen: C0398689; OMIM: 308230

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solute carrier family 2, facilitated glucose transporter member 2 isoform 1 [Hom...
solute carrier family 2, facilitated glucose transporter member 2 isoform 1 [Homo sapiens]
gi|4557851|ref|NP_000331.1|

Protein
dipeptidase PepV [Streptococcus pneumoniae]
dipeptidase PepV [Streptococcus pneumoniae]
gi|446482426|ref|WP_000560280.1|

Protein
Eyelid seborrheic keratosis
Eyelid seborrheic keratosis

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002243681	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 27, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15319456, 15358621, 16019685, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002243681

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 27, 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

The hyper IgM syndrome--an evolving story.

Etzioni A, Ochs HD.

Pediatr Res. 2004 Oct;56(4):519-25. Epub 2004 Aug 19. Review.

PubMed [citation]

PMID:: 15319456

Molecular analysis of a large cohort of patients with the hyper immunoglobulin M (IgM) syndrome.

Lee WI, Torgerson TR, Schumacher MJ, Yel L, Zhu Q, Ochs HD.

Blood. 2005 Mar 1;105(5):1881-90. Epub 2004 Sep 9.

PubMed [citation]

PMID:: 15358621

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002243681.3

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the CD40LG gene has been identified. Loss-of-function variants in CD40LG are known to be pathogenic (PMID: 15319456). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. A similar copy number variant has been observed in individual(s) with hyper IgM syndrome (PMID: 15358621, 16019685). For these reasons, this variant has been classified as Pathogenic.

#	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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