GRCh37/hg19 Xq25-28(chrX:124749464-155233731)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 29, 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:: RCV002474567.1

Allele description [Variation Report for GRCh37/hg19 Xq25-28(chrX:124749464-155233731)x1]

GRCh37/hg19 Xq25-28(chrX:124749464-155233731)x1

Genes:

AFF2:ALF transcription elongation factor 2 [Gene - OMIM - HGNC]
ABCD1:ATP binding cassette subfamily D member 1 [Gene - OMIM - HGNC]
ATP6AP1:ATPase H+ transporting accessory protein 1 [Gene - OMIM - HGNC]
ATP11C:ATPase phospholipid transporting 11C [Gene - OMIM - HGNC]
ATP2B3:ATPase plasma membrane Ca2+ transporting 3 [Gene - OMIM - HGNC]
BCAP31:B cell receptor associated protein 31 [Gene - OMIM - HGNC]
BCORL1:BCL6 corepressor like 1 [Gene - OMIM - HGNC]
BRCC3:BRCA1/BRCA2-containing complex subunit 3 [Gene - OMIM - HGNC]
CMC4:C-X9-C motif containing 4 [Gene - OMIM - HGNC]
CD40LG:CD40 ligand [Gene - OMIM - HGNC]
CD99L2:CD99 molecule like 2 [Gene - OMIM - HGNC]
CSAG3:CSAG family member 3 [Gene - OMIM - HGNC]
DCAF12L1:DDB1 and CUL4 associated factor 12 like 1 [Gene - HGNC]
DCAF12L2:DDB1 and CUL4 associated factor 12 like 2 [Gene - HGNC]
ELF4:E74 like ETS transcription factor 4 [Gene - OMIM - HGNC]
FAM3A:FAM3 metabolism regulating signaling molecule A [Gene - OMIM - HGNC]
FRMD7:FERM domain containing 7 [Gene - OMIM - HGNC]
FMR1-AS1:FMR1 antisense RNA 1 [Gene - OMIM - HGNC]
FMR1NB:FMR1 neighbor [Gene - HGNC]
FUNDC2:FUN14 domain containing 2 [Gene - OMIM - HGNC]
GPR101:G protein-coupled receptor 101 [Gene - OMIM - HGNC]
GPR119:G protein-coupled receptor 119 [Gene - OMIM - HGNC]
GPR50:G protein-coupled receptor 50 [Gene - OMIM - HGNC]
GDI1:GDP dissociation inhibitor 1 [Gene - OMIM - HGNC]
GPR50-AS1:GPR50 antisense RNA 1 [Gene - HGNC]
GAB3:GRB2 associated binding protein 3 [Gene - OMIM - HGNC]
H2AB1:H2A.B variant histone 1 [Gene - OMIM - HGNC]
H2AB2:H2A.B variant histone 2 [Gene - OMIM - HGNC]
H2AB3:H2A.B variant histone 3 [Gene - OMIM - HGNC]
HAUS7:HAUS augmin like complex subunit 7 [Gene - OMIM - HGNC]
HTATSF1:HIV-1 Tat specific factor 1 [Gene - OMIM - HGNC]
LAGE3:L antigen family member 3 [Gene - OMIM - HGNC]
L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]
LDOC1:LDOC1 regulator of NFKB signaling [Gene - OMIM - HGNC]
MAGEA10:MAGE family member A10 [Gene - OMIM - HGNC]
MAGEA11:MAGE family member A11 [Gene - OMIM - HGNC]
MAGEA12:MAGE family member A12 [Gene - OMIM - HGNC]
MAGEA1:MAGE family member A1 [Gene - OMIM - HGNC]
MAGEA2:MAGE family member A2 [Gene - OMIM - HGNC]
MAGEA2B:MAGE family member A2B [Gene - OMIM - HGNC]
MAGEA3:MAGE family member A3 [Gene - OMIM - HGNC]
MAGEA4:MAGE family member A4 [Gene - OMIM - HGNC]
MAGEA6:MAGE family member A6 [Gene - OMIM - HGNC]
MAGEA8:MAGE family member A8 [Gene - OMIM - HGNC]
MAGEA9:MAGE family member A9 [Gene - OMIM - HGNC]
MAGEA9B:MAGE family member A9B [Gene - OMIM - HGNC]
MAGEC1:MAGE family member C1 [Gene - OMIM - HGNC]
MAGEC2:MAGE family member C2 [Gene - OMIM - HGNC]
MAGEC3:MAGE family member C3 [Gene - OMIM - HGNC]
MPP1:MAGUK p55 scaffold protein 1 [Gene - OMIM - HGNC]
MAP7D3:MAP7 domain containing 3 [Gene - OMIM - HGNC]
MCF2:MCF.2 cell line derived transforming sequence [Gene - OMIM - HGNC]
NAA10:N-alpha-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
NSDHL:NAD(P) dependent steroid dehydrogenase-like [Gene - OMIM - HGNC]
OCRL:OCRL inositol polyphosphate-5-phosphatase [Gene - OMIM - HGNC]
PABIR2:PABIR family member 2 [Gene - HGNC]
PABIR3:PABIR family member 3 [Gene - HGNC]
PASD1:PAS domain containing repressor 1 [Gene - OMIM - HGNC]
PDZD4:PDZ domain containing 4 [Gene - OMIM - HGNC]
PHF6:PHD finger protein 6 [Gene - OMIM - HGNC]
PNMA3:PNMA family member 3 [Gene - OMIM - HGNC]
PNMA5:PNMA family member 5 [Gene - OMIM - HGNC]
PNMA6A:PNMA family member 6A [Gene - OMIM - HGNC]
PNMA6E:PNMA family member 6E [Gene - HGNC]
RAB33A:RAB33A, member RAS oncogene family [Gene - OMIM - HGNC]
RAB39B:RAB39B, member RAS oncogene family [Gene - OMIM - HGNC]
RAP2C:RAP2C, member of RAS oncogene family [Gene - OMIM - HGNC]
RBMX2:RNA binding motif protein X-linked 2 [Gene - HGNC]
RBMX:RNA binding motif protein X-linked [Gene - OMIM - HGNC]
ARHGEF6:Rac/Cdc42 guanine nucleotide exchange factor 6 [Gene - OMIM - HGNC]
ARHGAP36:Rho GTPase activating protein 36 [Gene - OMIM - HGNC]
ARHGAP4:Rho GTPase activating protein 4 [Gene - OMIM - HGNC]
SASH3:SAM and SH3 domain containing 3 [Gene - OMIM - HGNC]
SLITRK2:SLIT and NTRK like family member 2 [Gene - OMIM - HGNC]
SLITRK4:SLIT and NTRK like family member 4 [Gene - OMIM - HGNC]
SPANXA2:SPANX family member A2 [Gene - OMIM - HGNC]
SPANXB1:SPANX family member B1 [Gene - OMIM - HGNC]
SPANXC:SPANX family member C [Gene - OMIM - HGNC]
SPANXD:SPANX family member D [Gene - OMIM - HGNC]
SPANXN1:SPANX family member N1 [Gene - OMIM - HGNC]
SPANXN2:SPANX family member N2 [Gene - OMIM - HGNC]
SPANXN3:SPANX family member N3 [Gene - OMIM - HGNC]
SPANXN4:SPANX family member N4 [Gene - OMIM - HGNC]
SRPK3:SRSF protein kinase 3 [Gene - OMIM - HGNC]
SOX3:SRY-box transcription factor 3 [Gene - OMIM - HGNC]
SMARCA1:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 [Gene - OMIM - HGNC]
UTP14A:UTP14A small subunit processome component [Gene - OMIM - HGNC]
VBP1:VHL binding protein 1 [Gene - OMIM - HGNC]
XPNPEP2:X-prolyl aminopeptidase 2 [Gene - OMIM - HGNC]
ZFP92:ZFP92 zinc finger protein [Gene - HGNC]
ZIC3:Zic family member 3 [Gene - OMIM - HGNC]
ACTRT1:actin related protein T1 [Gene - OMIM - HGNC]
ADGRG4:adhesion G protein-coupled receptor G4 [Gene - OMIM - HGNC]
APLN:apelin [Gene - OMIM - HGNC]
AIFM1:apoptosis inducing factor mitochondria associated 1 [Gene - OMIM - HGNC]
AVPR2:arginine vasopressin receptor 2 [Gene - OMIM - HGNC]
BGN:biglycan [Gene - OMIM - HGNC]
BRS3:bombesin receptor subtype 3 [Gene - OMIM - HGNC]
CTAG1A:cancer/testis antigen 1A [Gene - OMIM - HGNC]
CTAG1B:cancer/testis antigen 1B [Gene - OMIM - HGNC]
CTAG2:cancer/testis antigen 2 [Gene - OMIM - HGNC]
CT55:cancer/testis antigen 55 [Gene - HGNC]
CT45A1:cancer/testis antigen family 45 member A1 [Gene - OMIM - HGNC]
CT45A2:cancer/testis antigen family 45 member A2 [Gene - OMIM - HGNC]
CT45A3:cancer/testis antigen family 45 member A3 [Gene - OMIM - HGNC]
CT45A5:cancer/testis antigen family 45 member A5 [Gene - OMIM - HGNC]
CT45A6:cancer/testis antigen family 45 member A6 [Gene - OMIM - HGNC]
CETN2:centrin 2 [Gene - OMIM - HGNC]
CDR1:cerebellar degeneration related 1 [Gene - OMIM - HGNC]
CLIC2:chloride intracellular channel 2 [Gene - OMIM - HGNC]
CSAG1:chondrosarcoma associated gene 1 [Gene - OMIM - HGNC]
CXorf51A:chromosome X open reading frame 51A [Gene - HGNC]
CXorf51B:chromosome X open reading frame 51B [Gene - HGNC]
CXorf66:chromosome X open reading frame 66 [Gene - HGNC]
F9:coagulation factor IX [Gene - OMIM - HGNC]
F8A1:coagulation factor VIII associated 1 [Gene - OMIM - HGNC]
F8A2:coagulation factor VIII associated 2 [Gene - HGNC]
F8A3:coagulation factor VIII associated 3 [Gene - HGNC]
F8:coagulation factor VIII [Gene - OMIM - HGNC]
CCDC160:coiled-coil domain containing 160 [Gene - HGNC]
CNGA2:cyclic nucleotide gated channel subunit alpha 2 [Gene - OMIM - HGNC]
CCNQ:cyclin Q [Gene - OMIM - HGNC]
DNASE1L1:deoxyribonuclease 1 like 1 [Gene - OMIM - HGNC]
DUSP9:dual specificity phosphatase 9 [Gene - OMIM - HGNC]
DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]
ENOX2:ecto-NOX disulfide-thiol exchanger 2 [Gene - OMIM - HGNC]
EMD:emerin [Gene - OMIM - HGNC]
EOLA1:endothelium and lymphocyte associated ASCH domain 1 [Gene - OMIM - HGNC]
EOLA2:endothelium and lymphocyte associated ASCH domain 2 [Gene - HGNC]
LOC100509091:extracellular matrix protein 2-like [Gene]
FAM50A:family with sequence similarity 50 member A [Gene - OMIM - HGNC]
FATE1:fetal and adult testis expressed 1 [Gene - OMIM - HGNC]
FGF13:fibroblast growth factor 13 [Gene - OMIM - HGNC]
FLNA:filamin A [Gene - OMIM - HGNC]
FHL1:four and a half LIM domains 1 [Gene - OMIM - HGNC]
FMR1:fragile X messenger ribonucleoprotein 1 [Gene - OMIM - HGNC]
GABRA3:gamma-aminobutyric acid type A receptor subunit alpha3 [Gene - OMIM - HGNC]
GABRE:gamma-aminobutyric acid type A receptor subunit epsilon [Gene - OMIM - HGNC]
GABRQ:gamma-aminobutyric acid type A receptor subunit theta [Gene - OMIM - HGNC]
G6PD:glucose-6-phosphate dehydrogenase [Gene - OMIM - HGNC]
GPC3:glypican 3 [Gene - OMIM - HGNC]
GPC4:glypican 4 [Gene - OMIM - HGNC]
HSFX1:heat shock transcription factor family, X-linked 1 [Gene - HGNC]
HSFX2:heat shock transcription factor family, X-linked 2 [Gene - HGNC]
HS6ST2:heparan sulfate 6-O-sulfotransferase 2 [Gene - OMIM - HGNC]
HMGB3:high mobility group box 3 [Gene - OMIM - HGNC]
HCFC1:host cell factor C1 [Gene - OMIM - HGNC]
HPRT1:hypoxanthine phosphoribosyltransferase 1 [Gene - OMIM - HGNC]
IDS:iduronate 2-sulfatase [Gene - OMIM - HGNC]
IGSF1:immunoglobulin superfamily member 1 [Gene - OMIM - HGNC]
IKBKG:inhibitor of nuclear factor kappa B kinase regulatory subunit gamma [Gene - OMIM - HGNC]
INTS6L:integrator complex subunit 6 like [Gene - HGNC]
IRAK1:interleukin 1 receptor associated kinase 1 [Gene - OMIM - HGNC]
IDH3G:isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [Gene - OMIM - HGNC]
MAMLD1:mastermind like domain containing 1 [Gene - OMIM - HGNC]
MTCP1:mature T cell proliferation 1 [Gene - OMIM - HGNC]
MMGT1:membrane magnesium transporter 1 [Gene - OMIM - HGNC]
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
MIR105-1:microRNA 105-1 [Gene - OMIM - HGNC]
MIR105-2:microRNA 105-2 [Gene - OMIM - HGNC]
MIR106A:microRNA 106a [Gene - OMIM - HGNC]
MIR19B2:microRNA 19b-2 [Gene - OMIM - HGNC]
MIR224:microRNA 224 [Gene - OMIM - HGNC]
MIR424:microRNA 424 [Gene - OMIM - HGNC]
MIR503:microRNA 503 [Gene - OMIM - HGNC]
MIR506:microRNA 506 [Gene - OMIM - HGNC]
MIR508:microRNA 508 [Gene - OMIM - HGNC]
MIR509-1:microRNA 509-1 [Gene - OMIM - HGNC]
MIR509-3:microRNA 509-3 [Gene - OMIM - HGNC]
MIR510:microRNA 510 [Gene - OMIM - HGNC]
MOSPD1:motile sperm domain containing 1 [Gene - OMIM - HGNC]
MBNL3:muscleblind like splicing regulator 3 [Gene - OMIM - HGNC]
MTM1:myotubularin 1 [Gene - OMIM - HGNC]
MTMR1:myotubularin related protein 1 [Gene - OMIM - HGNC]
OR13H1:olfactory receptor family 13 subfamily H member 1 [Gene - HGNC]
OPN1LW:opsin 1, long wave sensitive [Gene - OMIM - HGNC]
OPN1MW2:opsin 1, medium wave sensitive 2 [Gene - HGNC]
OPN1MW:opsin 1, medium wave sensitive [Gene - OMIM - HGNC]
PLAC1:placenta enriched 1 [Gene - OMIM - HGNC]
PLXNA3:plexin A3 [Gene - OMIM - HGNC]
PLXNB3:plexin B3 [Gene - OMIM - HGNC]
PNCK:pregnancy up-regulated nonubiquitous CaM kinase [Gene - OMIM - HGNC]
PRR32:proline rich 32 [Gene - HGNC]
PRRG3:proline rich and Gla domain 3 [Gene - OMIM - HGNC]
RENBP:renin binding protein [Gene - OMIM - HGNC]
RTL8A:retrotransposon Gag like 8A [Gene - HGNC]
RTL8B:retrotransposon Gag like 8B [Gene - HGNC]
RTL8C:retrotransposon Gag like 8C [Gene - OMIM - HGNC]
RPL10:ribosomal protein L10 [Gene - OMIM - HGNC]
SAGE1:sarcoma antigen 1 [Gene - OMIM - HGNC]
STK26:serine/threonine kinase 26 [Gene - OMIM - HGNC]
SSR4:signal sequence receptor subunit 4 [Gene - OMIM - HGNC]
SMIM10:small integral membrane protein 10 [Gene - HGNC]
SMIM9:small integral membrane protein 9 [Gene - HGNC]
SLC10A3:solute carrier family 10 member 3 [Gene - OMIM - HGNC]
SLC25A14:solute carrier family 25 member 14 [Gene - OMIM - HGNC]
SLC6A8:solute carrier family 6 member 8 [Gene - OMIM - HGNC]
SLC9A6:solute carrier family 9 member A6 [Gene - OMIM - HGNC]
SPANXA1:sperm protein associated with the nucleus, X-linked, family member A1 [Gene - OMIM - HGNC]
TAFAZZIN:tafazzin, phospholipid-lysophospholipid transacylase [Gene - OMIM - HGNC]
TEX28:testis expressed 28 [Gene - OMIM - HGNC]
TREX2:three prime repair exonuclease 2 [Gene - OMIM - HGNC]
TFDP3:transcription factor Dp family member 3 [Gene - OMIM - HGNC]
TKTL1:transketolase like 1 [Gene - OMIM - HGNC]
TMEM185A:transmembrane protein 185A [Gene - OMIM - HGNC]
TMEM187:transmembrane protein 187 [Gene - OMIM - HGNC]
TMLHE:trimethyllysine hydroxylase, epsilon [Gene - OMIM - HGNC]
UBE2NL:ubiquitin conjugating enzyme E2 N like (gene/pseudogene) [Gene - HGNC]
UBL4A:ubiquitin like 4A [Gene - OMIM - HGNC]
USP26:ubiquitin specific peptidase 26 [Gene - OMIM - HGNC]
VMA21:vacuolar ATPase assembly factor VMA21 [Gene - OMIM - HGNC]
VGLL1:vestigial like family member 1 [Gene - OMIM - HGNC]
ZDHHC9:zinc finger DHHC-type palmitoyltransferase 9 [Gene - OMIM - HGNC]
ZNF185:zinc finger protein 185 with LIM domain [Gene - OMIM - HGNC]
ZNF275:zinc finger protein 275 [Gene - HGNC]
ZNF280C:zinc finger protein 280C [Gene - HGNC]
ZNF449:zinc finger protein 449 [Gene - OMIM - HGNC]
ZNF75D:zinc finger protein 75D [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

Xq25-28

Genomic location:

ChrX: 124749464 - 155233731 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 Xq25-28(chrX:124749464-155233731)x1

HGVS:

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
SCV002771963	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Jun 29, 2022)	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

SCV002771963

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Jun 29, 2022)

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

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002771963.1

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

Description

The large Xq27.1q28 deletion at the distal long arm of the X chromosome involves numerous protein-coding genes. The phenotype of the Xq large deletion can range from partial Turner syndrome to minor menstrual abnormality. Microdeletions involving the FMR1 gene locus (3.5 Mb - 9.2 Mb, Xq27-Xq28) have been reported in females with developmental delays and/or other neurological feature such as epilepsy and intellectual disability. Some of these patients were reported to have random X-inactivation (Mol Syndromol. 2014 Feb;5(2):65-75. PMID: 24715853; Pediatrics. 2019 Sep;144(3):e20190599. PMID: 31439621; BMC Med Genet. 2013 May 1;14:49., PMID: 23634718). However, preferential inactivation of the abnormal X chromosome may result in relative normal to mild manifestations. A larger (32 Mb) de novo terminal Xq25q28 deletion was reported in a phenotypically normal 32 year old female except with early menopause. Data showed an extreme skewed X-inactivation of the abnormal X chromosome (Front Genet. 2020 Mar 4;11:101. PMID: 32194616).

#	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: Mar 26, 2023

ClinVar

Relating variation to medicine