NC_000003.11:g.(?_40924962)_(43760024_?)dup AND Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 30, 2021
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:: RCV001979130.2

Allele description

NC_000003.11:g.(?_40924962)_(43760024_?)dup

Genes:

HIGD1A:HIG1 hypoxia inducible domain family member 1A [Gene - OMIM - HGNC]
KRBOX1:KRAB box domain containing 1 [Gene - HGNC]
KRBOX1-AS1:KRBOX1 antisense RNA 1 [Gene - HGNC]
SEC22C:SEC22 homolog C, vesicle trafficking protein [Gene - OMIM - HGNC]
SNRK:SNF related kinase [Gene - OMIM - HGNC]
SS18L2:SS18 like 2 [Gene - OMIM - HGNC]
ABHD5:abhydrolase domain containing 5, lysophosphatidic acid acyltransferase [Gene - OMIM - HGNC]
ANO10:anoctamin 10 [Gene - OMIM - HGNC]
ACKR2:atypical chemokine receptor 2 [Gene - OMIM - HGNC]
CTNNB1:catenin beta 1 [Gene - OMIM - HGNC]
CCK:cholecystokinin [Gene - OMIM - HGNC]
CCDC13:coiled-coil domain containing 13 [Gene - HGNC]
CYP8B1:cytochrome P450 family 8 subfamily B member 1 [Gene - OMIM - HGNC]
GASK1A:golgi associated kinase 1A [Gene - HGNC]
HHATL:hedgehog acyltransferase like [Gene - OMIM - HGNC]
KLHL40:kelch like family member 40 [Gene - OMIM - HGNC]
LYZL4:lysozyme like 4 [Gene - OMIM - HGNC]
NKTR:natural killer cell triggering receptor [Gene - OMIM - HGNC]
POMGNT2:protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-) [Gene - OMIM - HGNC]
TRAK1:trafficking kinesin protein 1 [Gene - OMIM - HGNC]
ULK4:unc-51 like kinase 4 [Gene - OMIM - HGNC]
VIPR1:vasoactive intestinal peptide receptor 1 [Gene - OMIM - HGNC]
ZBTB47:zinc finger and BTB domain containing 47 [Gene - OMIM - HGNC]
ZNF662:zinc finger protein 662 [Gene - HGNC]

Variant type:

Duplication

Cytogenetic location:

3p22.1-21.33

Genomic location:

Chr3: 40924962 - 43760024 (on Assembly GRCh37)

Preferred name:

NC_000003.11:g.(?_40924962)_(43760024_?)dup

HGVS:

NC_000003.11:g.(?_40924962)_(43760024_?)dup

Condition(s)

Name:: Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 (MDDGA8)
Synonyms:: WALKER-WARBURG SYNDROME OR MUSCLE-EYE-BRAIN DISEASE, GTDC2-RELATED
Identifiers:: MONDO: MONDO:0013904; MedGen: C3553813; Orphanet: 899; OMIM: 614830

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002217990	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 30, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002217990

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 30, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

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, SCV002217990.2

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the POMGNT2 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. This variant has not been reported in the literature in individuals affected with POMGNT2-related conditions. 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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 13, 2023

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