NC_000023.10:g.(?_135067662)_(136652229_?)del AND Heterotaxy, visceral, 1, X-linked

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 21, 2023
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:: RCV001956452.6

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:: Heterotaxy, visceral, 1, X-linked (HTX1)
Synonyms:: Heterotaxy, visceral, X-linked; Dextrocardia with other cardiac malformations; Laterality, X-linked; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010607; MedGen: C1844020; Orphanet: 450; OMIM: 306955

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002238488	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 21, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 21465648, 24123890, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002238488

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 21, 2023)

germline

clinical testing

PubMed (3)
[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

From VACTERL-H to heterotaxy: variable expressivity of ZIC3-related disorders.

Chung B, Shaffer LG, Keating S, Johnson J, Casey B, Chitayat D.

Am J Med Genet A. 2011 May;155A(5):1123-8. doi: 10.1002/ajmg.a.33859. Epub 2011 Apr 4.

PubMed [citation]

PMID:: 21465648

Genetic and functional analyses of ZIC3 variants in congenital heart disease.

Cowan J, Tariq M, Ware SM.

Hum Mutat. 2014 Jan;35(1):66-75.

PubMed [citation]

PMID:: 24123890
PMCID:: PMC3946352

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002238488.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. A similar copy number variant has been observed in individual(s) with ZIC3-related conditions (PMID: 21465648). A gross deletion of the genomic region encompassing the full coding sequence of the ZIC3 gene has been identified. Loss-of-function variants in ZIC3 are known to be pathogenic (PMID: 24123890). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

#	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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