NC_000003.11:g.(?_57130421)_(57303715_?)dup AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 25, 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:: RCV003107767.5

Allele description [Variation Report for NC_000003.11:g.(?_57130421)_(57303715_?)dup]

NC_000003.11:g.(?_57130421)_(57303715_?)dup

Genes:: HESX1:HESX homeobox 1 [Gene - OMIM - HGNC]
APPL1:adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1 [Gene - OMIM - HGNC]
ASB14:ankyrin repeat and SOCS box containing 14 [Gene - HGNC]
IL17RD:interleukin 17 receptor D [Gene - OMIM - HGNC]
Variant type:: Duplication
Cytogenetic location:: 3p14.3
Genomic location:: Chr3: 57130421 - 57303715 (on Assembly GRCh37)
Preferred name:: NC_000003.11:g.(?_57130421)_(57303715_?)dup
HGVS:: NC_000003.11:g.(?_57130421)_(57303715_?)dup
This HGVS expression did not pass validation

Condition(s)

Name:: Septo-optic dysplasia sequence (SOD)
Synonyms:: Septo-optic dysplasia; De morsier syndrome; Septo-optic dysplasia with growth hormone deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008428; MedGen: C0338503; Orphanet: 3157; OMIM: 182230; Human Phenotype Ontology: HP:0100842

Name:: GROWTH HORMONE DEFICIENCY WITH PITUITARY ANOMALIES
Identifiers:: MedGen: C2750027

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003792527	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 25, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 32796691, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003792527

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 25, 2022)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Copy Number Variants Contributing to Combined Pituitary Hormone Deficiency.

Budny B, Karmelita-Katulska K, Stajgis M, Żemojtel T, Ruchała M, Ziemnicka K.

Int J Mol Sci. 2020 Aug 11;21(16). doi:pii: E5757. 10.3390/ijms21165757.

PubMed [citation]

PMID:: 32796691
PMCID:: PMC7461210

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, SCV003792527.3

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

Description

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. Isolated whole-gene copy number gains of HESX1 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 32796691). A copy number gain of the genomic region encompassing the full coding sequence of the HESX1 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome.

#	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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