GRCh37/hg19 9q22.2-31.1(chr9:93864974-106661581)x1 AND Gorlin syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 2, 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:: RCV002279743.2

Allele description [Variation Report for GRCh37/hg19 9q22.2-31.1(chr9:93864974-106661581)x1]

GRCh37/hg19 9q22.2-31.1(chr9:93864974-106661581)x1

Genes:

ALG2:ALG2 alpha-1,3/1,6-mannosyltransferase [Gene - OMIM - HGNC]
AUH:AU RNA binding methylglutaconyl-CoA hydratase [Gene - OMIM - HGNC]
BARX1:BARX homeobox 1 [Gene - OMIM - HGNC]
BICD2:BICD cargo adaptor 2 [Gene - OMIM - HGNC]
ERCC6L2:ERCC excision repair 6 like 2 [Gene - OMIM - HGNC]
FANCC:FA complementation group C [Gene - OMIM - HGNC]
FGD3:FYVE, RhoGEF and PH domain containing 3 [Gene - OMIM - HGNC]
MSANTD3-TMEFF1:MSANTD3-TMEFF1 readthrough [Gene - HGNC]
MSANTD3:Myb/SANT DNA binding domain containing 3 [Gene - HGNC]
NANS:N-acetylneuraminate synthase [Gene - OMIM - HGNC]
NUTM2F:NUT family member 2F [Gene - HGNC]
NUTM2G:NUT family member 2G [Gene - HGNC]
PHF2:PHD finger protein 2 [Gene - OMIM - HGNC]
SEC61B:SEC61 translocon subunit beta [Gene - OMIM - HGNC]
TBC1D2:TBC1 domain family member 2 [Gene - OMIM - HGNC]
WNK2:WNK lysine deficient protein kinase 2 [Gene - OMIM - HGNC]
XPA:XPA, DNA damage recognition and repair factor [Gene - OMIM - HGNC]
ANP32B:acidic nuclear phosphoprotein 32 family member B [Gene - OMIM - HGNC]
ALDOB:aldolase, fructose-bisphosphate B [Gene - OMIM - HGNC]
AOPEP:aminopeptidase O (putative) [Gene - OMIM - HGNC]
ANKS6:ankyrin repeat and sterile alpha motif domain containing 6 [Gene - OMIM - HGNC]
ASPN:asporin [Gene - OMIM - HGNC]
BAAT:bile acid-CoA:amino acid N-acyltransferase [Gene - OMIM - HGNC]
CARD19:caspase recruitment domain family member 19 [Gene - OMIM - HGNC]
CTSV:cathepsin V [Gene - OMIM - HGNC]
CAVIN4:caveolae associated protein 4 [Gene - OMIM - HGNC]
CDC14B:cell division cycle 14B [Gene - OMIM - HGNC]
CENPP:centromere protein P [Gene - OMIM - HGNC]
CCDC180:coiled-coil domain containing 180 [Gene - HGNC]
COL15A1:collagen type XV alpha 1 chain [Gene - OMIM - HGNC]
CORO2A:coronin 2A [Gene - OMIM - HGNC]
CYLC2:cylicin 2 [Gene - OMIM - HGNC]
ERP44:endoplasmic reticulum protein 44 [Gene - OMIM - HGNC]
ECM2:extracellular matrix protein 2 [Gene - OMIM - HGNC]
FAM120AOS:family with sequence similarity 120 member A opposite strand [Gene - HGNC]
FAM120A:family with sequence similarity 120 member A [Gene - OMIM - HGNC]
FOXE1:forkhead box E1 [Gene - OMIM - HGNC]
FBP1:fructose-bisphosphatase 1 [Gene - OMIM - HGNC]
FBP2:fructose-bisphosphatase 2 [Gene - OMIM - HGNC]
GABBR2:gamma-aminobutyric acid type B receptor subunit 2 [Gene - OMIM - HGNC]
GRIN3A:glutamate ionotropic receptor NMDA type subunit 3A [Gene - OMIM - HGNC]
HEMGN:hemogen [Gene - OMIM - HGNC]
HABP4:hyaluronan binding protein 4 [Gene - OMIM - HGNC]
HSD17B3:hydroxysteroid 17-beta dehydrogenase 3 [Gene - OMIM - HGNC]
IPPK:inositol-pentakisphosphate 2-kinase [Gene - OMIM - HGNC]
INVS:inversin [Gene - OMIM - HGNC]
IARS1:isoleucyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
MFSD14B:major facilitator superfamily domain containing 14B [Gene - OMIM - HGNC]
MIR23B:microRNA 23b [Gene - OMIM - HGNC]
MIR24-1:microRNA 24-1 [Gene - OMIM - HGNC]
MIR27B:microRNA 27b [Gene - OMIM - HGNC]
MIRLET7A1:microRNA let-7a-1 [Gene - OMIM - HGNC]
MIRLET7D:microRNA let-7d [Gene - OMIM - HGNC]
MIRLET7F1:microRNA let-7f-1 [Gene - OMIM - HGNC]
MRPL50:mitochondrial ribosomal protein L50 [Gene - OMIM - HGNC]
NINJ1:ninjurin 1 [Gene - OMIM - HGNC]
NCBP1:nuclear cap binding protein subunit 1 [Gene - OMIM - HGNC]
NFIL3:nuclear factor, interleukin 3 regulated [Gene - OMIM - HGNC]
NR4A3:nuclear receptor subfamily 4 group A member 3 [Gene - OMIM - HGNC]
NOL8:nucleolar protein 8 [Gene - OMIM - HGNC]
OGN:osteoglycin [Gene - OMIM - HGNC]
OMD:osteomodulin [Gene - OMIM - HGNC]
PTCH1:patched 1 [Gene - OMIM - HGNC]
PRXL2C:peroxiredoxin like 2C [Gene - HGNC]
GALNT12:polypeptide N-acetylgalactosaminyltransferase 12 [Gene - OMIM - HGNC]
PGAP4:post-GPI attachment to proteins GalNAc transferase 4 [Gene - OMIM - HGNC]
PPP3R2:protein phosphatase 3 regulatory subunit B, beta [Gene - OMIM - HGNC]
PTPDC1:protein tyrosine phosphatase domain containing 1 [Gene - HGNC]
ROR2:receptor tyrosine kinase like orphan receptor 2 [Gene - OMIM - HGNC]
RNF20:ring finger protein 20 [Gene - OMIM - HGNC]
SPTLC1:serine palmitoyltransferase long chain base subunit 1 [Gene - OMIM - HGNC]
PRSS47:serine protease 47 [Gene - HGNC]
SLC35D2:solute carrier family 35 member D2 [Gene - OMIM - HGNC]
SUSD3:sushi domain containing 3 [Gene - OMIM - HGNC]
STX17:syntaxin 17 [Gene - OMIM - HGNC]
TRMO:tRNA methyltransferase O [Gene - HGNC]
TEX10:testis expressed 10 [Gene - OMIM - HGNC]
TSTD2:thiosulfate sulfurtransferase like domain containing 2 [Gene - HGNC]
TGFBR1:transforming growth factor beta receptor 1 [Gene - OMIM - HGNC]
TMEFF1:transmembrane protein with EGF like and two follistatin like domains 1 [Gene - OMIM - HGNC]
TRIM14:tripartite motif containing 14 [Gene - OMIM - HGNC]
TMOD1:tropomodulin 1 [Gene - OMIM - HGNC]
TDRD7:tudor domain containing 7 [Gene - OMIM - HGNC]
ZNF169:zinc finger protein 169 [Gene - OMIM - HGNC]
ZNF189:zinc finger protein 189 [Gene - OMIM - HGNC]
ZNF367:zinc finger protein 367 [Gene - OMIM - HGNC]
ZNF484:zinc finger protein 484 [Gene - HGNC]
ZNF510:zinc finger protein 510 [Gene - OMIM - HGNC]
ZNF782:zinc finger protein 782 [Gene - HGNC]

Variant type:

copy number loss

Cytogenetic location:

9q22.2-31.1

Genomic location:

Chr9: 93864974 - 106661581 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 9q22.2-31.1(chr9:93864974-106661581)x1

HGVS:

NC_000009.11:g.(?_93864974)_(106661581_?)del

Condition(s)

Name:: Gorlin syndrome
Synonyms:: Basal cell nevus syndrome
Identifiers:: MONDO: MONDO:0007187; MedGen: C0004779; Orphanet: 377; OMIM: PS109400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002098072	Centro Nacional de Genética Medica "Dr. Eduardo E. Castilla", Administración Nacional de Laboratorios e Institutos de Salud	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Feb 2, 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

SCV002098072

Centro Nacional de Genética Medica "Dr. Eduardo E. Castilla", Administración Nacional de Laboratorios e Institutos de Salud

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Feb 2, 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	yes	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 Centro Nacional de Genética Medica "Dr. Eduardo E. Castilla", Administración Nacional de Laboratorios e Institutos de Salud, SCV002098072.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	blood	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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Relating variation to medicine