NC_000023.10:g.(?_63409759)_(71933728_?)dup AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 2024
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:: RCV004582202.2

Allele description [Variation Report for NC_000023.10:g.(?_63409759)_(71933728_?)dup]

NC_000023.10:g.(?_63409759)_(71933728_?)dup

Genes:

AMER1:APC membrane recruitment protein 1 [Gene - OMIM - HGNC]
CXCR3:C-X-C motif chemokine receptor 3 [Gene - OMIM - HGNC]
CITED1:Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 [Gene - OMIM - HGNC]
ERCC6L:ERCC excision repair 6 like, spindle assembly checkpoint helicase [Gene - OMIM - HGNC]
LAS1L:LAS1 like ribosome biogenesis factor [Gene - OMIM - HGNC]
NALF2:NALCN channel auxiliary factor 2 [Gene - HGNC]
NHSL2:NHS like 2 [Gene - OMIM - HGNC]
OGT:O-linked N-acetylglucosamine (GlcNAc) transferase [Gene - OMIM - HGNC]
OTUD6A:OTU deubiquitinase 6A [Gene - OMIM - HGNC]
PDZD11:PDZ domain containing 11 [Gene - OMIM - HGNC]
RAB41:RAB41, member RAS oncogene family [Gene - HGNC]
STARD8:StAR related lipid transfer domain containing 8 [Gene - OMIM - HGNC]
TAF1:TATA-box binding protein associated factor 1 [Gene - OMIM - HGNC]
VSIG4:V-set and immunoglobulin domain containing 4 [Gene - OMIM - HGNC]
YIPF6:Yip1 domain family member 6 [Gene - OMIM - HGNC]
AWAT1:acyl-CoA wax alcohol acyltransferase 1 [Gene - OMIM - HGNC]
AWAT2:acyl-CoA wax alcohol acyltransferase 2 [Gene - OMIM - HGNC]
AR:androgen receptor [Gene - OMIM - HGNC]
ASB12:ankyrin repeat and SOCS box containing 12 [Gene - OMIM - HGNC]
ARR3:arrestin 3 [Gene - OMIM - HGNC]
CXorf49:chromosome X open reading frame 49 [Gene - HGNC]
CXorf49B:chromosome X open reading frame 49B [Gene - HGNC]
CXorf65:chromosome X open reading frame 65 [Gene - HGNC]
DGAT2L6:diacylglycerol O-acyltransferase 2 like 6 [Gene - OMIM - HGNC]
DLG3:discs large MAGUK scaffold protein 3 [Gene - OMIM - HGNC]
EDA2R:ectodysplasin A2 receptor [Gene - OMIM - HGNC]
EDA:ectodysplasin A [Gene - OMIM - HGNC]
EFNB1:ephrin B1 [Gene - OMIM - HGNC]
FOXO4:forkhead box O4 [Gene - OMIM - HGNC]
GJB1:gap junction protein beta 1 [Gene - OMIM - HGNC]
GCNA:germ cell nuclear acidic peptidase [Gene - OMIM - HGNC]
GDPD2:glycerophosphodiester phosphodiesterase domain containing 2 [Gene - OMIM - HGNC]
HEPH:hephaestin [Gene - OMIM - HGNC]
HDAC8:histone deacetylase 8 [Gene - OMIM - HGNC]
IGBP1:immunoglobulin binding protein 1 [Gene - OMIM - HGNC]
ITGB1BP2:integrin subunit beta 1 binding protein 2 [Gene - OMIM - HGNC]
IL2RG:interleukin 2 receptor subunit gamma [Gene - OMIM - HGNC]
KIF4A:kinesin family member 4A [Gene - OMIM - HGNC]
MED12:mediator complex subunit 12 [Gene - OMIM - HGNC]
MIR223:microRNA 223 [Gene - OMIM - HGNC]
MSN:moesin [Gene - OMIM - HGNC]
MTMR8:myotubularin related protein 8 [Gene - OMIM - HGNC]
NLGN3:neuroligin 3 [Gene - OMIM - HGNC]
NONO:non-POU domain containing octamer binding [Gene - OMIM - HGNC]
OPHN1:oligophrenin 1 [Gene - OMIM - HGNC]
PIN4:peptidylprolyl cis/trans isomerase, NIMA-interacting 4 [Gene - OMIM - HGNC]
PHKA1:phosphorylase kinase regulatory subunit alpha 1 [Gene - OMIM - HGNC]
PJA1:praja ring finger ubiquitin ligase 1 [Gene - OMIM - HGNC]
P2RY4:pyrimidinergic receptor P2Y4 [Gene - OMIM - HGNC]
RTL5:retrotransposon Gag like 5 [Gene - HGNC]
RPS4X:ribosomal protein S4 X-linked [Gene - OMIM - HGNC]
SLC7A3:solute carrier family 7 member 3 [Gene - OMIM - HGNC]
SNX12:sorting nexin 12 [Gene - OMIM - HGNC]
TEX11:testis expressed 11 [Gene - OMIM - HGNC]
ZC4H2:zinc finger C4H2-type containing [Gene - OMIM - HGNC]
ZC3H12B:zinc finger CCCH-type containing 12B [Gene - OMIM - HGNC]
ZMYM3:zinc finger MYM-type containing 3 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xq11.2-13.2

Genomic location:

ChrX: 63409759 - 71933728 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_63409759)_(71933728_?)dup

HGVS:

NC_000023.10:g.(?_63409759)_(71933728_?)dup

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
SCV005066325	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 25, 2024)	unknown	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

SCV005066325

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 25, 2024)

unknown

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	unknown	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV005066325.1

#	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 AMER1 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 AMER1-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	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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