GRCh37/hg19 5p15.33-15.32(chr5:22149-4641409)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000446677.4

Allele description [Variation Report for GRCh37/hg19 5p15.33-15.32(chr5:22149-4641409)x1]

GRCh37/hg19 5p15.33-15.32(chr5:22149-4641409)x1

Genes:

CLPTM1L:CLPTM1 like [Gene - OMIM - HGNC]
EXOC3-AS1:EXOC3 antisense RNA 1 [Gene - HGNC]
IRX2-DT:IRX2 divergent transcript [Gene - OMIM - HGNC]
NDUFS6:NADH:ubiquinone oxidoreductase subunit S6 [Gene - OMIM - HGNC]
NKD2:NKD inhibitor of WNT signaling pathway 2 [Gene - OMIM - HGNC]
AHRR:aryl hydrocarbon receptor repressor [Gene - OMIM - HGNC]
BRD9:bromodomain containing 9 [Gene - OMIM - HGNC]
CEP72:centrosomal protein 72 [Gene - OMIM - HGNC]
CCDC127:coiled-coil domain containing 127 [Gene - HGNC]
EXOC3:exocyst complex component 3 [Gene - OMIM - HGNC]
IRX1:iroquois homeobox 1 [Gene - OMIM - HGNC]
IRX2:iroquois homeobox 2 [Gene - OMIM - HGNC]
IRX4:iroquois homeobox 4 [Gene - OMIM - HGNC]
LRRC14B:leucine rich repeat containing 14B [Gene - HGNC]
LPCAT1:lysophosphatidylcholine acyltransferase 1 [Gene - OMIM - HGNC]
MRPL36:mitochondrial ribosomal protein L36 [Gene - OMIM - HGNC]
PLEKHG4B:pleckstrin homology and RhoGEF domain containing G4B [Gene - OMIM - HGNC]
PDCD6:programmed cell death 6 [Gene - OMIM - HGNC]
SLC12A7:solute carrier family 12 member 7 [Gene - OMIM - HGNC]
SLC6A18:solute carrier family 6 member 18 [Gene - OMIM - HGNC]
SLC6A19:solute carrier family 6 member 19 [Gene - OMIM - HGNC]
SLC6A3:solute carrier family 6 member 3 [Gene - OMIM - HGNC]
SLC9A3:solute carrier family 9 member A3 [Gene - OMIM - HGNC]
SDHA:succinate dehydrogenase complex flavoprotein subunit A [Gene - OMIM - HGNC]
TERT:telomerase reverse transcriptase [Gene - OMIM - HGNC]
TRIP13:thyroid hormone receptor interactor 13 [Gene - OMIM - HGNC]
TPPP:tubulin polymerization promoting protein [Gene - OMIM - HGNC]
ZDHHC11:zinc finger DHHC-type containing 11 [Gene - HGNC]
ZDHHC11B:zinc finger DHHC-type containing 11B [Gene - HGNC]

Variant type:

copy number loss

Cytogenetic location:

5p15.33-15.32

Genomic location:

Chr5: 22149 - 4641409 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 5p15.33-15.32(chr5:22149-4641409)x1

HGVS:

NC_000005.9:g.(?_22149)_(4641409_?)del

Links:

dbVar: nssv13650582; dbVar: nsv2772151

Observations:

Condition(s)

Name:: See cases [See the Variation display for details]
Identifiers:

Recent activity

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penicillin-binding protein [Oenococcus oeni]
penicillin-binding protein [Oenococcus oeni]
gi|488910284|ref|WP_002821359.1|

Protein
Bacillus thuringiensis strain 27-3, whole genome shotgun sequencing project
Bacillus thuringiensis strain 27-3, whole genome shotgun sequencing project
gi|1802427465|gb|NKAT00000000.1|NKA 0000

Nucleotide
Homo sapiens protein tyrosine phosphatase non-receptor type 20 (PTPN20), transcr...
Homo sapiens protein tyrosine phosphatase non-receptor type 20 (PTPN20), transcript variant 1, mRNA
gi|1890261247|ref|NM_001042357.5|

Nucleotide
Microbe sample from Halorhodospira halochloris
Microbe sample from Halorhodospira halochloris

biosample
Homo sapiens mRNA; cDNA DKFZp761A1124 (from clone DKFZp761A1124)
Homo sapiens mRNA; cDNA DKFZp761A1124 (from clone DKFZp761A1124)
gi|7669974|emb|AL353937.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000499885	ISCA Site 6 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	no assertion criteria provided	Pathogenic	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

SCV000499885

ISCA Site 6

See additional submitters

no assertion criteria provided

Pathogenic

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	not provided	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]

PMID:: 20466091
PMCID:: PMC2869000

Details of each submission

From ISCA Site 6, SCV000499885.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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