NC_000002.11:g.(?_173420879)_(174232392_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 2, 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:: RCV004583847.2

Allele description [Variation Report for NC_000002.11:g.(?_173420879)_(174232392_?)del]

NC_000002.11:g.(?_173420879)_(174232392_?)del

Genes:: RAPGEF4:Rap guanine nucleotide exchange factor 4 [Gene - OMIM - HGNC]
CDCA7:cell division cycle associated 7 [Gene - OMIM - HGNC]
MAP3K20:mitogen-activated protein kinase kinase kinase 20 [Gene - OMIM - HGNC]
PDK1:pyruvate dehydrogenase kinase 1 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 2q31.1
Genomic location:: Chr2: 173420879 - 174232392 (on Assembly GRCh37)
Preferred name:: NC_000002.11:g.(?_173420879)_(174232392_?)del
HGVS:: NC_000002.11:g.(?_173420879)_(174232392_?)del
This HGVS expression did not pass validation

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
SCV005064965	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 2, 2022)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 27816943, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005064965

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 2, 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

Recessive mutations in the kinase ZAK cause a congenital myopathy with fibre type disproportion.

Vasli N, Harris E, Karamchandani J, Bareke E, Majewski J, Romero NB, Stojkovic T, Barresi R, Tasfaout H, Charlton R, Malfatti E, Bohm J, Marini-Bettolo C, Choquet K, Dicaire MJ, Shao YH, Topf A, O'Ferrall E, Eymard B, Straub V, Blanco G, Lochmüller H, et al.

Brain. 2017 Jan;140(1):37-48. doi: 10.1093/brain/aww257. Epub 2016 Nov 5.

PubMed [citation]

PMID:: 27816943
PMCID:: PMC5226058

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, SCV005064965.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with MAP3K20-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the MAP3K20 gene has been identified. Loss-of-function variants in MAP3K20 are known to be pathogenic (PMID: 27816943). 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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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