GRCh37/hg19 Yp11.31-q12(chrY:2654852-59031480)x2 AND See cases

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 31, 2013
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:: RCV000148271.2

Allele description

GRCh37/hg19 Yp11.31-q12(chrY:2654852-59031480)x2

Genes:

DDX3Y:DEAD-box helicase 3 Y-linked [Gene - OMIM - HGNC]
PRORY:PRORY Y-linked lncRNA [Gene - HGNC]
PRY2:PTPN13 like Y-linked 2 [Gene - OMIM - HGNC]
PRY:PTPN13 like Y-linked [Gene - OMIM - HGNC]
RBMY1A1:RNA binding motif protein Y-linked family 1 member A1 [Gene - OMIM - HGNC]
RBMY1B:RNA binding motif protein Y-linked family 1 member B [Gene - HGNC]
RBMY1D:RNA binding motif protein Y-linked family 1 member D [Gene - HGNC]
RBMY1E:RNA binding motif protein Y-linked family 1 member E [Gene - HGNC]
RBMY1F:RNA binding motif protein Y-linked family 1 member F [Gene - HGNC]
RBMY1J:RNA binding motif protein Y-linked family 1 member J [Gene - HGNC]
TGIF2LY:TGFB induced factor homeobox 2 like Y-linked [Gene - OMIM - HGNC]
AMELY:amelogenin Y-linked [Gene - OMIM - HGNC]
BPY2:basic charge Y-linked 2 [Gene - OMIM - HGNC]
BPY2B:basic charge Y-linked 2B [Gene - HGNC]
BPY2C:basic charge Y-linked 2C [Gene - HGNC]
CDY1:chromodomain Y-linked 1 [Gene - OMIM - HGNC]
CDY2A:chromodomain Y-linked 2A [Gene - OMIM - HGNC]
DAZ1:deleted in azoospermia 1 [Gene - OMIM - HGNC]
DAZ2:deleted in azoospermia 2 [Gene - OMIM - HGNC]
DAZ3:deleted in azoospermia 3 [Gene - OMIM - HGNC]
DAZ4:deleted in azoospermia 4 [Gene - OMIM - HGNC]
EIF1AY:eukaryotic translation initiation factor 1A Y-linked [Gene - OMIM - HGNC]
FAM197Y1P:family with sequence similarity 197 Y-linked member 1, pseudogene [Gene - HGNC]
FAM197Y10:family with sequence similarity 197 Y-linked member 10 [Gene - HGNC]
FAM197Y9:family with sequence similarity 197 Y-linked member 9 [Gene - HGNC]
HSFY1:heat shock transcription factor Y-linked 1 [Gene - OMIM - HGNC]
HSFY2:heat shock transcription factor Y-linked 2 [Gene - HGNC]
KDM5D:lysine demethylase 5D [Gene - OMIM - HGNC]
NLGN4Y:neuroligin 4 Y-linked [Gene - OMIM - HGNC]
PCDH11Y:protocadherin 11 Y-linked [Gene - OMIM - HGNC]
RPS4Y1:ribosomal protein S4 Y-linked 1 [Gene - OMIM - HGNC]
RPS4Y2:ribosomal protein S4 Y-linked 2 [Gene - OMIM - HGNC]
SRY:sex determining region Y [Gene - OMIM - HGNC]
TSPY10:testis specific protein Y-linked 10 [Gene - HGNC]
TSPY1:testis specific protein Y-linked 1 [Gene - OMIM - HGNC]
TSPY2:testis specific protein Y-linked 2 [Gene - HGNC]
TSPY3:testis specific protein Y-linked 3 [Gene - HGNC]
TSPY4:testis specific protein Y-linked 4 [Gene - HGNC]
TSPY8:testis specific protein Y-linked 8 [Gene - HGNC]
TTTY10:testis-specific transcript, Y-linked 10 [Gene - HGNC]
TTTY11:testis-specific transcript, Y-linked 11 [Gene - HGNC]
TTTY12:testis-specific transcript, Y-linked 12 [Gene - HGNC]
TTTY13:testis-specific transcript, Y-linked 13 [Gene - HGNC]
TTTY13B:testis-specific transcript, Y-linked 13B [Gene - HGNC]
TTTY14:testis-specific transcript, Y-linked 14 [Gene - HGNC]
TTTY15:testis-specific transcript, Y-linked 15 [Gene - HGNC]
TTTY16:testis-specific transcript, Y-linked 16 [Gene - HGNC]
TTTY17A:testis-specific transcript, Y-linked 17A [Gene - OMIM - HGNC]
TTTY17B:testis-specific transcript, Y-linked 17B [Gene - HGNC]
TTTY17C:testis-specific transcript, Y-linked 17C [Gene - HGNC]
TTTY18:testis-specific transcript, Y-linked 18 [Gene - HGNC]
TTTY19:testis-specific transcript, Y-linked 19 [Gene - HGNC]
TTTY1:testis-specific transcript, Y-linked 1 [Gene - HGNC]
TTTY1B:testis-specific transcript, Y-linked 1B [Gene - HGNC]
TTTY20:testis-specific transcript, Y-linked 20 [Gene - HGNC]
TTTY21:testis-specific transcript, Y-linked 21 [Gene - HGNC]
TTTY21B:testis-specific transcript, Y-linked 21B [Gene - HGNC]
TTTY22:testis-specific transcript, Y-linked 22 [Gene - HGNC]
TTTY23:testis-specific transcript, Y-linked 23 [Gene - HGNC]
TTTY23B:testis-specific transcript, Y-linked 23B [Gene - HGNC]
TTTY2:testis-specific transcript, Y-linked 2 [Gene - HGNC]
TTTY2B:testis-specific transcript, Y-linked 2B [Gene - HGNC]
TTTY3:testis-specific transcript, Y-linked 3 [Gene - OMIM - HGNC]
TTTY3B:testis-specific transcript, Y-linked 3B [Gene - HGNC]
TTTY4:testis-specific transcript, Y-linked 4 [Gene - OMIM - HGNC]
TTTY4B:testis-specific transcript, Y-linked 4B [Gene - HGNC]
TTTY4C:testis-specific transcript, Y-linked 4C [Gene - HGNC]
TTTY5:testis-specific transcript, Y-linked 5 [Gene - OMIM - HGNC]
TTTY6:testis-specific transcript, Y-linked 6 [Gene - OMIM - HGNC]
TTTY6B:testis-specific transcript, Y-linked 6B [Gene - HGNC]
TTTY7:testis-specific transcript, Y-linked 7 [Gene - HGNC]
TTTY7B:testis-specific transcript, Y-linked 7B [Gene - HGNC]
TTTY8:testis-specific transcript, Y-linked 8 [Gene - HGNC]
TTTY8B:testis-specific transcript, Y-linked 8B [Gene - HGNC]
TTTY9A:testis-specific transcript, Y-linked 9A [Gene - HGNC]
TTTY9B:testis-specific transcript, Y-linked 9B [Gene - HGNC]
TMSB4Y:thymosin beta 4 Y-linked [Gene - OMIM - HGNC]
TBL1Y:transducin beta like 1 Y-linked [Gene - OMIM - HGNC]
USP9Y:ubiquitin specific peptidase 9 Y-linked [Gene - OMIM - HGNC]
UTY:ubiquitously transcribed tetratricopeptide repeat containing, Y-linked [Gene - OMIM - HGNC]
VCY1B:variable charge Y-linked 1B [Gene - OMIM - HGNC]
VCY:variable charge Y-linked [Gene - OMIM - HGNC]
ZFY:zinc finger protein Y-linked [Gene - OMIM - HGNC]

Variant type:

copy number gain

Cytogenetic location:

Yp11.31-q12

Genomic location:

Preferred name:

GRCh37/hg19 Yp11.31-q12(chrY:2654852-59031480)x2

HGVS:

NC_000024.8:g.(?_2714852)_(57440868_?)dup
NC_000024.9:g.(?_2654852)_(59031480_?)dup

Links:

dbVar: nssv579289; dbVar: nssv579290; dbVar: nssv579294; dbVar: nssv579295; dbVar: nssv579296; dbVar: nssv579298; dbVar: nssv579299; dbVar: nsv1067785

Observations:

Condition(s)

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

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hypothetical protein EMIHUDRAFT_465602 [Emiliania huxleyi CCMP1516]
hypothetical protein EMIHUDRAFT_465602 [Emiliania huxleyi CCMP1516]
gi|551545750|ref|XP_005760844.1||gn _WGS:AHAL|EMIHUDRAFT_465602

Protein
Choloepus didactylus isolate Cd3 cytochrome b (Cyt_b) gene, partial cds; mitocho...
Choloepus didactylus isolate Cd3 cytochrome b (Cyt_b) gene, partial cds; mitochondrial
gi|2284916635|gb|ON316834.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000077632	ISCA site 4 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Jan 31, 2013)	not provided	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

SCV000077632

ISCA site 4

See additional submitters

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))

Pathogenic
(Jan 31, 2013)

not provided

clinical testing

PubMed (1)
[See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	not provided	yes	7	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, et al.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

PubMed [citation]

PMID:: 21844811
PMCID:: PMC3661946

Details of each submission

From ISCA site 4, SCV000077632.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)
2	not provided	1	not provided	not provided	clinical testing	PubMed (1)
3	not provided	1	not provided	not provided	clinical testing	PubMed (1)
4	not provided	1	not provided	not provided	clinical testing	PubMed (1)
5	not provided	1	not provided	not provided	clinical testing	PubMed (1)
6	not provided	1	not provided	not provided	clinical testing	PubMed (1)
7	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	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
2	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
3	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
4	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
5	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
6	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided
7	not provided	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: Jul 8, 2023

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