NC_000002.11:g.(?_69240632)_(74779761_?)dup AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 30, 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:: RCV003122858.2

Allele description

NC_000002.11:g.(?_69240632)_(74779761_?)dup

Genes:

ALMS1:ALMS1 centrosome and basal body associated protein [Gene - OMIM - HGNC]
ANTXR1:ANTXR cell adhesion molecule 1 [Gene - OMIM - HGNC]
AAK1:AP2 associated kinase 1 [Gene - OMIM - HGNC]
ATP6V1B1:ATPase H+ transporting V1 subunit B1 [Gene - OMIM - HGNC]
AUP1:AUP1 lipid droplet regulating VLDL assembly factor [Gene - OMIM - HGNC]
CLEC4F:C-type lectin domain family 4 member F [Gene - OMIM - HGNC]
CD207:CD207 molecule [Gene - OMIM - HGNC]
DQX1:DEAQ-box RNA dependent ATPase 1 [Gene - HGNC]
FBXO41:F-box protein 41 [Gene - OMIM - HGNC]
HTRA2:HtrA serine peptidase 2 [Gene - OMIM - HGNC]
INO80B:INO80 complex subunit B [Gene - OMIM - HGNC]
MPHOSPH10:M-phase phosphoprotein 10 [Gene - OMIM - HGNC]
MXD1:MAX dimerization protein 1 [Gene - OMIM - HGNC]
MOB1A:MOB kinase activator 1A [Gene - OMIM - HGNC]
NAGK:N-acetylglucosamine kinase [Gene - OMIM - HGNC]
NAT8:N-acetyltransferase 8 (putative) [Gene - OMIM - HGNC]
NAT8B:N-acetyltransferase 8B (putative, gene/pseudogene) [Gene - OMIM - HGNC]
NFU1:NFU1 iron-sulfur cluster scaffold [Gene - OMIM - HGNC]
RAB11FIP5:RAB11 family interacting protein 5 [Gene - OMIM - HGNC]
SMYD5:SMYD family member 5 [Gene - OMIM - HGNC]
STAMBP:STAM binding protein [Gene - OMIM - HGNC]
TLX2:T cell leukemia homeobox 2 [Gene - OMIM - HGNC]
TIA1:TIA1 cytotoxic granule associated RNA binding protein [Gene - OMIM - HGNC]
TPRKB:TP53RK binding protein [Gene - OMIM - HGNC]
WDR54:WD repeat domain 54 [Gene - HGNC]
WBP1:WW domain binding protein 1 [Gene - OMIM - HGNC]
ACTG2:actin gamma 2, smooth muscle [Gene - OMIM - HGNC]
ADD2:adducin 2 [Gene - OMIM - HGNC]
ANKRD53:ankyrin repeat domain 53 [Gene - OMIM - HGNC]
ANXA4:annexin A4 [Gene - OMIM - HGNC]
ASPRV1:aspartic peptidase retroviral like 1 [Gene - OMIM - HGNC]
BOLA3:bolA family member 3 [Gene - OMIM - HGNC]
CCT7:chaperonin containing TCP1 subunit 7 [Gene - OMIM - HGNC]
C2orf42:chromosome 2 open reading frame 42 [Gene - HGNC]
C2orf78:chromosome 2 open reading frame 78 [Gene - HGNC]
C2orf81:chromosome 2 open reading frame 81 [Gene - HGNC]
CCDC142:coiled-coil domain containing 142 [Gene - HGNC]
CYP26B1:cytochrome P450 family 26 subfamily B member 1 [Gene - OMIM - HGNC]
DGUOK:deoxyguanosine kinase [Gene - OMIM - HGNC]
DOK1:docking protein 1 [Gene - OMIM - HGNC]
DUSP11:dual specificity phosphatase 11 [Gene - OMIM - HGNC]
DCTN1:dynactin subunit 1 [Gene - OMIM - HGNC]
DYSF:dysferlin [Gene - OMIM - HGNC]
EGR4:early growth response 4 [Gene - OMIM - HGNC]
EMX1:empty spiracles homeobox 1 [Gene - OMIM - HGNC]
EXOC6B:exocyst complex component 6B [Gene - OMIM - HGNC]
FAM136A:family with sequence similarity 136 member A [Gene - OMIM - HGNC]
FIGLA:folliculogenesis specific bHLH transcription factor [Gene - OMIM - HGNC]
GMCL1:germ cell-less 1, spermatogenesis associated [Gene - OMIM - HGNC]
GFPT1:glutamine--fructose-6-phosphate transaminase 1 [Gene - OMIM - HGNC]
LBX2:ladybird homeobox 2 [Gene - OMIM - HGNC]
LOXL3:lysyl oxidase like 3 [Gene - OMIM - HGNC]
MOGS:mannosyl-oligosaccharide glucosidase [Gene - OMIM - HGNC]
MTHFD2:methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase [Gene - OMIM - HGNC]
MCEE:methylmalonyl-CoA epimerase [Gene - OMIM - HGNC]
MRPL53:mitochondrial ribosomal protein L53 [Gene - OMIM - HGNC]
NOTO:notochord homeobox [Gene - HGNC]
PAIP2B:poly(A) binding protein interacting protein 2B [Gene - OMIM - HGNC]
PCBP1:poly(rC) binding protein 1 [Gene - OMIM - HGNC]
PCGF1:polycomb group ring finger 1 [Gene - OMIM - HGNC]
PCYOX1:prenylcysteine oxidase 1 [Gene - OMIM - HGNC]
PRADC1:protease associated domain containing 1 [Gene - OMIM - HGNC]
RTKN:rhotekin [Gene - OMIM - HGNC]
SPR:sepiapterin reductase [Gene - OMIM - HGNC]
SFXN5:sideroflexin 5 [Gene - OMIM - HGNC]
SNRNP27:small nuclear ribonucleoprotein U4/U6.U5 subunit 27 [Gene - OMIM - HGNC]
SNRPG:small nuclear ribonucleoprotein polypeptide G [Gene - OMIM - HGNC]
SLC4A5:solute carrier family 4 member 5 [Gene - OMIM - HGNC]
TEX261:testis expressed 261 [Gene - OMIM - HGNC]
TET3:tet methylcytosine dioxygenase 3 [Gene - OMIM - HGNC]
TTC31:tetratricopeptide repeat domain 31 [Gene - HGNC]
TGFA:transforming growth factor alpha [Gene - OMIM - HGNC]
VAX2:ventral anterior homeobox 2 [Gene - OMIM - HGNC]
ZNF638:zinc finger protein 638 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

2p13.3-13.1

Genomic location:

Chr2: 69240632 - 74779761 (on Assembly GRCh37)

Preferred name:

NC_000002.11:g.(?_69240632)_(74779761_?)dup

HGVS:

NC_000002.11:g.(?_69240632)_(74779761_?)dup

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003795718	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 30, 2022)	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

SCV003795718

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 30, 2022)

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, SCV003795718.1

#	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 ANTXR1 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 ANTXR1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: Oct 14, 2023

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