NC_000023.10:g.(?_46466387)_(51241672_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 5, 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:: RCV003154905.2

Allele description [Variation Report for NC_000023.10:g.(?_46466387)_(51241672_?)del]

NC_000023.10:g.(?_46466387)_(51241672_?)del

Genes:

ARAF:A-Raf proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
AKAP4:A-kinase anchoring protein 4 [Gene - OMIM - HGNC]
EBP:EBP cholestenol delta-isomerase [Gene - OMIM - HGNC]
ERAS:ES cell expressed Ras [Gene - OMIM - HGNC]
ELK1:ETS transcription factor ELK1 [Gene - OMIM - HGNC]
FTSJ1:FtsJ RNA 2'-O-methyltransferase 1 [Gene - OMIM - HGNC]
GAGE12B:G antigen 12B [Gene - HGNC]
GAGE12C:G antigen 12C [Gene - OMIM - HGNC]
GAGE12D:G antigen 12D [Gene - OMIM - HGNC]
GAGE12E:G antigen 12E [Gene - OMIM - HGNC]
GAGE12F:G antigen 12F [Gene - OMIM - HGNC]
GAGE12G:G antigen 12G [Gene - OMIM - HGNC]
GAGE12H:G antigen 12H [Gene - OMIM - HGNC]
GAGE12I:G antigen 12I [Gene - OMIM - HGNC]
GAGE12J:G antigen 12J [Gene - OMIM - HGNC]
GAGE13:G antigen 13 [Gene - OMIM - HGNC]
GAGE1:G antigen 1 [Gene - OMIM - HGNC]
GAGE2A:G antigen 2A [Gene - OMIM - HGNC]
GAGE2B:G antigen 2B [Gene - OMIM - HGNC]
GAGE2C:G antigen 2C [Gene - OMIM - HGNC]
GAGE2D:G antigen 2D [Gene - OMIM - HGNC]
GAGE2E:G antigen 2E [Gene - OMIM - HGNC]
GAGE8:G antigen 8 [Gene - OMIM - HGNC]
GPKOW:G-patch domain and KOW motifs [Gene - OMIM - HGNC]
GATA1:GATA binding protein 1 [Gene - OMIM - HGNC]
GRIPAP1:GRIP1 associated protein 1 [Gene - OMIM - HGNC]
MAGIX:MAGI family member, X-linked [Gene - HGNC]
NDUFB11:NADH:ubiquinone oxidoreductase subunit B11 [Gene - OMIM - HGNC]
OTUD5:OTU deubiquitinase 5 [Gene - OMIM - HGNC]
PAGE1:PAGE family member 1 [Gene - OMIM - HGNC]
PAGE4:PAGE family member 4 [Gene - OMIM - HGNC]
PRAF2:PRA1 domain family member 2 [Gene - OMIM - HGNC]
PIM2:Pim-2 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
RBM10:RNA binding motif protein 10 [Gene - OMIM - HGNC]
RBM3:RNA binding motif protein 3 [Gene - OMIM - HGNC]
RP2:RP2 activator of ARL3 GTPase [Gene - OMIM - HGNC]
SSX1:SSX family member 1 [Gene - OMIM - HGNC]
SSX3:SSX family member 3 [Gene - OMIM - HGNC]
SSX4:SSX family member 4 [Gene - OMIM - HGNC]
SSX4B:SSX family member 4B [Gene - HGNC]
SSX5:SSX family member 5 [Gene - OMIM - HGNC]
SUV39H1:SUV39H1 histone lysine methyltransferase [Gene - OMIM - HGNC]
TBC1D25:TBC1 domain family member 25 [Gene - OMIM - HGNC]
TIMP1:TIMP metallopeptidase inhibitor 1 [Gene - OMIM - HGNC]
WAS:WASP actin nucleation promoting factor [Gene - OMIM - HGNC]
WDR13:WD repeat domain 13 [Gene - OMIM - HGNC]
WDR45:WD repeat domain 45 [Gene - OMIM - HGNC]
BMP15:bone morphogenetic protein 15 [Gene - OMIM - HGNC]
CACNA1F:calcium voltage-gated channel subunit alpha1 F [Gene - OMIM - HGNC]
CLCN5:chloride voltage-gated channel 5 [Gene - OMIM - HGNC]
CCDC120:coiled-coil domain containing 120 [Gene - OMIM - HGNC]
CCDC22:coiled-coil domain containing 22 [Gene - OMIM - HGNC]
CFP:complement factor properdin [Gene - OMIM - HGNC]
CCNB3:cyclin B3 [Gene - OMIM - HGNC]
CDK16:cyclin dependent kinase 16 [Gene - OMIM - HGNC]
DGKK:diacylglycerol kinase kappa [Gene - OMIM - HGNC]
FOXP3:forkhead box P3 [Gene - OMIM - HGNC]
GLOD5:glyoxalase domain containing 5 [Gene - OMIM - HGNC]
HDAC6:histone deacetylase 6 [Gene - OMIM - HGNC]
INE1:inactivation escape 1 [Gene - OMIM - HGNC]
JADE3:jade family PHD finger 3 [Gene - OMIM - HGNC]
LINC01560:long intergenic non-protein coding RNA 1560 [Gene - HGNC]
MIR502:microRNA 502 [Gene - OMIM - HGNC]
MIR532:microRNA 532 [Gene - OMIM - HGNC]
NUDT10:nudix hydrolase 10 [Gene - OMIM - HGNC]
NUDT11:nudix hydrolase 11 [Gene - OMIM - HGNC]
PQBP1:polyglutamine binding protein 1 [Gene - OMIM - HGNC]
PORCN:porcupine O-acyltransferase [Gene - OMIM - HGNC]
KCND1:potassium voltage-gated channel subfamily D member 1 [Gene - OMIM - HGNC]
PRICKLE3:prickle planar cell polarity protein 3 [Gene - OMIM - HGNC]
PCSK1N:proprotein convertase subtilisin/kexin type 1 inhibitor [Gene - OMIM - HGNC]
PPP1R3F:protein phosphatase 1 regulatory subunit 3F [Gene - OMIM - HGNC]
PLP2:proteolipid protein 2 [Gene - OMIM - HGNC]
RGN:regucalcin [Gene - OMIM - HGNC]
SHROOM4:shroom family member 4 [Gene - OMIM - HGNC]
SLC35A2:solute carrier family 35 member A2 [Gene - OMIM - HGNC]
SLC38A5:solute carrier family 38 member 5 [Gene - OMIM - HGNC]
SLC9A7:solute carrier family 9 member A7 [Gene - OMIM - HGNC]
SPACA5:sperm acrosome associated 5 [Gene - OMIM - HGNC]
SPACA5B:sperm acrosome associated 5B [Gene - HGNC]
SYN1:synapsin I [Gene - OMIM - HGNC]
SYP:synaptophysin [Gene - OMIM - HGNC]
TFE3:transcription factor binding to IGHM enhancer 3 [Gene - OMIM - HGNC]
TIMM17B:translocase of inner mitochondrial membrane 17B [Gene - OMIM - HGNC]
UBA1:ubiquitin like modifier activating enzyme 1 [Gene - OMIM - HGNC]
USP11:ubiquitin specific peptidase 11 [Gene - OMIM - HGNC]
USP27X:ubiquitin specific peptidase 27 X-linked [Gene - OMIM - HGNC]
UXT:ubiquitously expressed prefoldin like chaperone [Gene - OMIM - HGNC]
ZNF157:zinc finger protein 157 [Gene - OMIM - HGNC]
ZNF182:zinc finger protein 182 [Gene - OMIM - HGNC]
ZNF41:zinc finger protein 41 [Gene - OMIM - HGNC]
ZNF630:zinc finger protein 630 [Gene - OMIM - HGNC]
ZNF81:zinc finger protein 81 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp11.23-11.22

Genomic location:

ChrX: 46466387 - 51241672 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_46466387)_(51241672_?)del

HGVS:

NC_000023.10:g.(?_46466387)_(51241672_?)del

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
SCV003843946	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 5, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 10391218, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003843946

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 5, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Mutations in a delta 8-delta 7 sterol isomerase in the tattered mouse and X-linked dominant chondrodysplasia punctata. [email protected].

Derry JM, Gormally E, Means GD, Zhao W, Meindl A, Kelley RI, Boyd Y, Herman GE.

Nat Genet. 1999 Jul;22(3):286-90.

PubMed [citation]

PMID:: 10391218

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, SCV003843946.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the EBP gene has been identified. Loss-of-function variants in EBP are known to be pathogenic (PMID: 10391218). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with EBP-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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: Sep 29, 2024

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