NC_000012.11:g.(?_6438478)_(7362819_?)dup AND Temtamy syndrome

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 9, 2020
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:: RCV001365174.1

Allele description

NC_000012.11:g.(?_6438478)_(7362819_?)dup

Genes:

CD27:CD27 molecule [Gene - OMIM - HGNC]
CD4:CD4 molecule [Gene - OMIM - HGNC]
COPS7A:COP9 signalosome subunit 7A [Gene - OMIM - HGNC]
EMG1:EMG1 N1-specific pseudouridine methyltransferase [Gene - OMIM - HGNC]
GNB3:G protein subunit beta 3 [Gene - OMIM - HGNC]
GPR162:G protein-coupled receptor 162 [Gene - HGNC]
NOP2:NOP2 nucleolar protein [Gene - OMIM - HGNC]
PIANP:PILR alpha associated neural protein [Gene - OMIM - HGNC]
TAPBPL:TAP binding protein like [Gene - OMIM - HGNC]
TNFRSF1A:TNF receptor superfamily member 1A [Gene - OMIM - HGNC]
ACRBP:acrosin binding protein [Gene - OMIM - HGNC]
ATN1:atrophin 1 [Gene - OMIM - HGNC]
CLSTN3:calsyntenin 3 [Gene - OMIM - HGNC]
CDCA3:cell division cycle associated 3 [Gene - OMIM - HGNC]
CHD4:chromodomain helicase DNA binding protein 4 [Gene - OMIM - HGNC]
C12orf57:chromosome 12 open reading frame 57 [Gene - OMIM - HGNC]
C1RL:complement C1r subcomponent like [Gene - OMIM - HGNC]
C1R:complement C1r [Gene - OMIM - HGNC]
C1S:complement C1s [Gene - OMIM - HGNC]
ENO2:enolase 2 [Gene - OMIM - HGNC]
GAPDH:glyceraldehyde-3-phosphate dehydrogenase [Gene - OMIM - HGNC]
ING4:inhibitor of growth family member 4 [Gene - OMIM - HGNC]
IFFO1:intermediate filament family orphan 1 [Gene - OMIM - HGNC]
LRRC23:leucine rich repeat containing 23 [Gene - HGNC]
LAG3:lymphocyte activating 3 [Gene - OMIM - HGNC]
LTBR:lymphotoxin beta receptor [Gene - OMIM - HGNC]
LPAR5:lysophosphatidic acid receptor 5 [Gene - OMIM - HGNC]
LPCAT3:lysophosphatidylcholine acyltransferase 3 [Gene - OMIM - HGNC]
MIR141:microRNA 141 [Gene - OMIM - HGNC]
MIR200C:microRNA 200c [Gene - OMIM - HGNC]
MRPL51:mitochondrial ribosomal protein L51 [Gene - OMIM - HGNC]
MLF2:myeloid leukemia factor 2 [Gene - OMIM - HGNC]
NCAPD2:non-SMC condensin I complex subunit D2 [Gene - OMIM - HGNC]
PTMS:parathymosin [Gene - OMIM - HGNC]
PEX5:peroxisomal biogenesis factor 5 [Gene - OMIM - HGNC]
PHB2:prohibitin 2 [Gene - OMIM - HGNC]
P3H3:prolyl 3-hydroxylase 3 [Gene - OMIM - HGNC]
PTPN6:protein tyrosine phosphatase non-receptor type 6 [Gene - OMIM - HGNC]
RBP5:retinol binding protein 5 [Gene - OMIM - HGNC]
SCNN1A:sodium channel epithelial 1 subunit alpha [Gene - OMIM - HGNC]
SPSB2:splA/ryanodine receptor domain and SOCS box containing 2 [Gene - OMIM - HGNC]
TPI1:triosephosphate isomerase 1 [Gene - OMIM - HGNC]
USP5:ubiquitin specific peptidase 5 [Gene - OMIM - HGNC]
VAMP1:vesicle associated membrane protein 1 [Gene - OMIM - HGNC]
ZNF384:zinc finger protein 384 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

12p13.31

Genomic location:

Chr12: 6438478 - 7362819 (on Assembly GRCh37)

Preferred name:

NC_000012.11:g.(?_6438478)_(7362819_?)dup

HGVS:

NC_000012.11:g.(?_6438478)_(7362819_?)dup

Condition(s)

Name:: Temtamy syndrome (TEMTYS)
Synonyms:: Dysmorphism, corpus callosum agenesis and colobomas; Craniofacial dysmorphism with ocular coloboma absent corpus callosum and aortic dilatation; MENTAL RETARDATION WITH OR WITHOUT CRANIOFACIAL DYSMORPHISM, OCULAR COLOBOMA, OR ABNORMAL CORPUS CALLOSUM
Identifiers:: MONDO: MONDO:0009033; MedGen: C1857512; Orphanet: 1777; OMIM: 218340

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001561430	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 9, 2020)	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

SCV001561430

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 9, 2020)

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, SCV001561430.1

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the C12orf57 gene. 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 with C12orf57-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: Mar 26, 2023

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