NC_000004.11:g.(?_171788098)_(175916898_?)del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 13, 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:: RCV004580861.1

Allele description

NC_000004.11:g.(?_171788098)_(175916898_?)del

Genes:

HPGD:15-hydroxyprostaglandin dehydrogenase [Gene - OMIM - HGNC]
ADAM29:ADAM metallopeptidase domain 29 [Gene - OMIM - HGNC]
FBXO8:F-box protein 8 [Gene - OMIM - HGNC]
SAP30:Sin3A associated protein 30 [Gene - OMIM - HGNC]
CEP44:centrosomal protein 44 [Gene - OMIM - HGNC]
GLRA3:glycine receptor alpha 3 [Gene - OMIM - HGNC]
HAND2:heart and neural crest derivatives expressed 2 [Gene - OMIM - HGNC]
HMGB2:high mobility group box 2 [Gene - OMIM - HGNC]
GALNT7:polypeptide N-acetylgalactosaminyltransferase 7 [Gene - OMIM - HGNC]
GALNTL6:polypeptide N-acetylgalactosaminyltransferase like 6 [Gene - OMIM - HGNC]
SCRG1:stimulator of chondrogenesis 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q33-34.1

Genomic location:

Chr4: 171788098 - 175916898 (on Assembly GRCh37)

Preferred name:

NC_000004.11:g.(?_171788098)_(175916898_?)del

HGVS:

NC_000004.11:g.(?_171788098)_(175916898_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005064885	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 2022)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 32134193, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005064885

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 2022)

unknown

clinical testing

PubMed (2)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Haploinsufficiency of the basic helix-loop-helix transcription factor HAND2 causes congenital heart defects.

Cohen ASA, Simotas C, Webb BD, Shi H, Khan WA, Edelmann L, Scott SA, Singh R.

Am J Med Genet A. 2020 May;182(5):1263-1267. doi: 10.1002/ajmg.a.61537. Epub 2020 Mar 5.

PubMed [citation]

PMID:: 32134193

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 Invitae, SCV005064885.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Isolated whole-gene deletion of HAND2 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 32134193). A gross deletion of the genomic region encompassing the full coding sequence of the HAND2 gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in HAND2 cause disease. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. 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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 7, 2024

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