Single allele AND Neurodevelopmental disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 9, 2019
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:: RCV000787381.2

Allele description [Variation Report for Single allele]

Genes:

ATP5MC2:ATP synthase membrane subunit c locus 2 [Gene - OMIM - HGNC]
COPZ1:COPI coat complex subunit zeta 1 [Gene - OMIM - HGNC]
HOTAIR:HOX transcript antisense RNA [Gene - OMIM - HGNC]
HOXC13-AS:HOXC13 antisense RNA [Gene - HGNC]
SP1:Sp1 transcription factor [Gene - OMIM - HGNC]
TARBP2:TARBP2 subunit of RISC loading complex [Gene - OMIM - HGNC]
ATF7:activating transcription factor 7 [Gene - OMIM - HGNC]
AMHR2:anti-Mullerian hormone receptor type 2 [Gene - OMIM - HGNC]
CALCOCO1:calcium binding and coiled-coil domain 1 [Gene - HGNC]
CBX5:chromobox 5 [Gene - OMIM - HGNC]
HNRNPA1:heterogeneous nuclear ribonucleoprotein A1 [Gene - OMIM - HGNC]
HOXC10:homeobox C10 [Gene - OMIM - HGNC]
HOXC11:homeobox C11 [Gene - OMIM - HGNC]
HOXC12:homeobox C12 [Gene - OMIM - HGNC]
HOXC13:homeobox C13 [Gene - OMIM - HGNC]
HOXC4:homeobox C4 [Gene - OMIM - HGNC]
HOXC5:homeobox C5 [Gene - OMIM - HGNC]
HOXC6:homeobox C6 [Gene - OMIM - HGNC]
HOXC8:homeobox C8 [Gene - OMIM - HGNC]
HOXC9:homeobox C9 [Gene - OMIM - HGNC]
MIR148B:microRNA 148b [Gene - OMIM - HGNC]
MIR196A2:microRNA 196a-2 [Gene - OMIM - HGNC]
MAP3K12:mitogen-activated protein kinase kinase kinase 12 [Gene - OMIM - HGNC]
NPFF:neuropeptide FF-amide peptide precursor [Gene - OMIM - HGNC]
NFE2:nuclear factor, erythroid 2 [Gene - OMIM - HGNC]
PCBP2:poly(rC) binding protein 2 [Gene - OMIM - HGNC]
PRR13:proline rich 13 [Gene - OMIM - HGNC]
SMUG1:single-strand-selective monofunctional uracil-DNA glycosylase 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q13.13

Genomic location:

Chr12: 53784698 - 54741363 (on Assembly GRCh37)

HGVS:

NC_000012.11:g.53784698_54741363del

Condition(s)

Name:: Neurodevelopmental disorder
Identifiers:: MONDO: MONDO:0700092; MeSH: D065886; MedGen: C1535926

Recent activity

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enoyl-CoA hydratase-related protein [Parasphingorhabdus flavimaris]
enoyl-CoA hydratase-related protein [Parasphingorhabdus flavimaris]
gi|1861781889|ref|WP_176278227.1|

Protein
transglycosylase SLT domain-containing protein [Parasphingorhabdus flavimaris]
transglycosylase SLT domain-containing protein [Parasphingorhabdus flavimaris]
gi|2693050090|ref|WP_335647695.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000926343	Rare Disease Group, Clinical Genetics, Karolinska Institutet	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 9, 2019)	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

SCV000926343

Rare Disease Group, Clinical Genetics, Karolinska Institutet

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 9, 2019)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Rare Disease Group, Clinical Genetics, Karolinska Institutet, SCV000926343.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 14, 2023

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