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GRCh38/hg38 Yp11.32-q12(chrY:10701-57189762) AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 24, 2012
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:
RCV000135689.5

Allele description [Variation Report for GRCh38/hg38 Yp11.32-q12(chrY:10701-57189762)]

GRCh38/hg38 Yp11.32-q12(chrY:10701-57189762)

Genes:
  • AKAP17A:A-kinase anchoring protein 17A [Gene - OMIM - OMIM - HGNC]
  • ASMTL-AS1:ASMTL antisense RNA 1 [Gene - HGNC]
  • LOC106128902:AZFa HERV15yq1 recombination region [Gene]
  • LOC108004538:AZFa HERV15yq2 recombination region [Gene]
  • LOC106144557:AZFb P1.2 recombination region [Gene]
  • LOC108868752:AZFb P4.1 recombination region [Gene]
  • LOC106144556:AZFb P5.1 recombination region [Gene]
  • LOC108863624:AZFb P5.2 recombination region [Gene]
  • LOC106144558:AZFc P1.1 recombination region [Gene]
  • LOC108868753:AZFc P1.1b recombination region [Gene]
  • LOC126057109:BRD4-independent group 4 enhancer GRCh37_chrY:22253264-22254463 [Gene]
  • LOC126057110:BRD4-independent group 4 enhancer GRCh37_chrY:22277369-22278568 [Gene]
  • LOC126057111:BRD4-independent group 4 enhancer GRCh37_chrY:22280323-22281522 [Gene]
  • LOC126057112:BRD4-independent group 4 enhancer GRCh37_chrY:22299473-22300672 [Gene]
  • LOC126057113:BRD4-independent group 4 enhancer GRCh37_chrY:22316202-22317401 [Gene]
  • CD99:CD99 molecule (Xg blood group) [Gene - OMIM - OMIM - HGNC]
  • CNE-2:CNE-2 enhancer upstream of SHOX [Gene]
  • CNE-3:CNE-3 enhancer upstream of SHOX [Gene]
  • CNE-5:CNE-5 enhancer upstream of SHOX [Gene]
  • CNE4:CNE4 enhancer downstream of SHOX [Gene]
  • CNE5:CNE5 enhancer downstream of SHOX [Gene]
  • CNE6:CNE6 enhancer downstream of SHOX [Gene]
  • CNE7:CNE7 enhancer downstream of SHOX [Gene]
  • CNE8:CNE8 enhancer downstream of SHOX [Gene]
  • CNE9:CNE9 enhancer downstream of SHOX [Gene]
  • DDX3Y:DEAD-box helicase 3 Y-linked [Gene - OMIM - HGNC]
  • GTPBP6:GTP binding protein 6 (putative) [Gene - OMIM - HGNC]
  • LOC106144609:IR4 Yp recombination region [Gene]
  • LOC106144610:IR4 Yq recombination region [Gene]
  • LOC126057107:MED14-independent group 3 enhancer GRCh37_chrY:16452370-16453569 [Gene]
  • LOC126057108:MED14-independent group 3 enhancer GRCh37_chrY:19155795-19156994 [Gene]
  • LOC126057114:MED14-independent group 3 enhancer GRCh37_chrY:22339850-22341049 [Gene]
  • LOC126057106:MED14-independent group 3 enhancer GRCh37_chrY:6975278-6976477 [Gene]
  • NLGN4Y-AS1:NLGN4Y antisense RNA 1 [Gene - HGNC]
  • P2RY8:P2Y receptor family member 8 [Gene - OMIM - HGNC]
  • LOC126057105:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrY:6931456-6932655 [Gene]
  • 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]
  • LOC108251802:SHOX downstream enhancer, distal recombination region [Gene]
  • LOC108251803:SHOX downstream enhancer, proximal recombination region [Gene]
  • SHOX:SHOX homeobox [Gene - OMIM - OMIM - HGNC]
  • LOC108178989:SRY promoter region [Gene]
  • TGIF2LY:TGFB induced factor homeobox 2 like Y-linked [Gene - OMIM - HGNC]
  • ZFY-AS1:ZFY antisense RNA 1 [Gene - HGNC]
  • ASMTL:acetylserotonin O-methyltransferase like [Gene - OMIM - OMIM - HGNC]
  • ASMT:acetylserotonin O-methyltransferase [Gene - OMIM - 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]
  • CDY1B:chromodomain Y-linked 1B [Gene - HGNC]
  • CDY2A:chromodomain Y-linked 2A [Gene - OMIM - HGNC]
  • CDY2B:chromodomain Y-linked 2B [Gene - HGNC]
  • CSF2RA:colony stimulating factor 2 receptor subunit alpha [Gene - OMIM - OMIM - HGNC]
  • CRLF2:cytokine receptor like factor 2 [Gene - OMIM - OMIM - HGNC]
  • DHRSX:dehydrogenase/reductase X-linked [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]
  • FAM197Y2:family with sequence similarity 197 Y-linked member 2 [Gene - HGNC]
  • FAM197Y3:family with sequence similarity 197 Y-linked member 3 [Gene - HGNC]
  • FAM197Y4:family with sequence similarity 197 Y-linked member 4 [Gene - HGNC]
  • FAM197Y5:family with sequence similarity 197 Y-linked member 5 [Gene - HGNC]
  • FAM197Y6:family with sequence similarity 197 Y-linked member 6 [Gene - HGNC]
  • FAM197Y7:family with sequence similarity 197 Y-linked member 7 [Gene - HGNC]
  • FAM197Y8:family with sequence similarity 197 Y-linked member 8 [Gene - HGNC]
  • FAM197Y9:family with sequence similarity 197 Y-linked member 9 [Gene - HGNC]
  • FAM224A:family with sequence similarity 224 member A [Gene - HGNC]
  • FAM224B:family with sequence similarity 224 member B [Gene - HGNC]
  • FAM41AY1:family with sequence similarity 41 member A, Y-linked 1 [Gene - HGNC]
  • FAM41AY2:family with sequence similarity 41 member A, Y-linked 2 [Gene - HGNC]
  • HSFY1:heat shock transcription factor Y-linked 1 [Gene - OMIM - HGNC]
  • HSFY2:heat shock transcription factor Y-linked 2 [Gene - HGNC]
  • IL3RA:interleukin 3 receptor subunit alpha [Gene - OMIM - OMIM - HGNC]
  • IL9R:interleukin 9 receptor [Gene - OMIM - HGNC]
  • LINC00102:long intergenic non-protein coding RNA 102 [Gene - HGNC]
  • LINC00106:long intergenic non-protein coding RNA 106 [Gene - HGNC]
  • LINC00278:long intergenic non-protein coding RNA 278 [Gene - HGNC]
  • LINC00279:long intergenic non-protein coding RNA 279 [Gene - HGNC]
  • LINC00280:long intergenic non-protein coding RNA 280 [Gene - HGNC]
  • LINC00685:long intergenic non-protein coding RNA 685 [Gene - HGNC]
  • KDM5D:lysine demethylase 5D [Gene - OMIM - HGNC]
  • LOC107522039:meiotic recombination hotspot PAR2 [Gene]
  • LOC107838685:meiotic recombination hotspot PAR2A [Gene]
  • LOC107652445:meiotic recombination hotspot SHOX [Gene]
  • MIR12120:microRNA 12120 [Gene - HGNC]
  • MIR3690:microRNA 3690 [Gene - HGNC]
  • MIR6089:microRNA 6089 [Gene - HGNC]
  • MIR9985:microRNA 9985 [Gene - HGNC]
  • NLGN4Y:neuroligin 4 Y-linked [Gene - OMIM - HGNC]
  • PLCXD1:phosphatidylinositol specific phospholipase C X domain containing 1 [Gene - OMIM - HGNC]
  • PPP2R3B:protein phosphatase 2 regulatory subunit B''beta [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]
  • SLC25A6:solute carrier family 25 member 6 [Gene - OMIM - OMIM - HGNC]
  • SPRY3:sprouty RTK signaling antagonist 3 [Gene - OMIM - HGNC]
  • TTTY10:testis expressed transcript, Y-linked 10 [Gene - HGNC]
  • TTTY11:testis expressed transcript, Y-linked 11 [Gene - HGNC]
  • TTTY12:testis expressed transcript, Y-linked 12 [Gene - HGNC]
  • TTTY13:testis expressed transcript, Y-linked 13 [Gene - HGNC]
  • TTTY14:testis expressed transcript, Y-linked 14 [Gene - HGNC]
  • TTTY15:testis expressed transcript, Y-linked 15 [Gene - HGNC]
  • TTTY16:testis expressed transcript, Y-linked 16 [Gene - HGNC]
  • TTTY17A:testis expressed transcript, Y-linked 17A [Gene - OMIM - HGNC]
  • TTTY17B:testis expressed transcript, Y-linked 17B [Gene - HGNC]
  • TTTY17C:testis expressed transcript, Y-linked 17C [Gene - HGNC]
  • TTTY18:testis expressed transcript, Y-linked 18 [Gene - HGNC]
  • TTTY19:testis expressed transcript, Y-linked 19 [Gene - HGNC]
  • TTTY1:testis expressed transcript, Y-linked 1 [Gene - HGNC]
  • TTTY1B:testis expressed transcript, Y-linked 1B [Gene - HGNC]
  • TTTY20:testis expressed transcript, Y-linked 20 [Gene - HGNC]
  • TTTY21:testis expressed transcript, Y-linked 21 [Gene - HGNC]
  • TTTY21B:testis expressed transcript, Y-linked 21B [Gene - HGNC]
  • TTTY22:testis expressed transcript, Y-linked 22 [Gene - HGNC]
  • TTTY23:testis expressed transcript, Y-linked 23 [Gene - HGNC]
  • TTTY23B:testis expressed transcript, Y-linked 23B [Gene - HGNC]
  • TTTY2:testis expressed transcript, Y-linked 2 [Gene - HGNC]
  • TTTY2B:testis expressed transcript, Y-linked 2B [Gene - HGNC]
  • TTTY3:testis expressed transcript, Y-linked 3 [Gene - OMIM - HGNC]
  • TTTY3B:testis expressed transcript, Y-linked 3B [Gene - HGNC]
  • TTTY4:testis expressed transcript, Y-linked 4 [Gene - OMIM - HGNC]
  • TTTY4B:testis expressed transcript, Y-linked 4B [Gene - HGNC]
  • TTTY4C:testis expressed transcript, Y-linked 4C [Gene - HGNC]
  • TTTY5:testis expressed transcript, Y-linked 5 [Gene - OMIM - HGNC]
  • TTTY6:testis expressed transcript, Y-linked 6 [Gene - OMIM - HGNC]
  • TTTY6B:testis expressed transcript, Y-linked 6B [Gene - HGNC]
  • TTTY7:testis expressed transcript, Y-linked 7 [Gene - HGNC]
  • TTTY7B:testis expressed transcript, Y-linked 7B [Gene - HGNC]
  • TTTY8:testis expressed transcript, Y-linked 8 [Gene - HGNC]
  • TTTY8B:testis expressed transcript, Y-linked 8B [Gene - HGNC]
  • TTTY9A:testis expressed transcript, Y-linked 9A [Gene - HGNC]
  • TTTY9B:testis expressed transcript, Y-linked 9B [Gene - 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]
  • TSPY9:testis specific protein Y-linked 9 [Gene - HGNC]
  • TTTY13B:testis-specific transcript, Y-linked 13B [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]
  • LOC101929148:uncharacterized LOC101929148 [Gene]
  • VCY1B:variable charge Y-linked 1B [Gene - OMIM - HGNC]
  • VCY:variable charge Y-linked [Gene - OMIM - HGNC]
  • VAMP7:vesicle associated membrane protein 7 [Gene - OMIM - HGNC]
  • ZBED1:zinc finger BED-type containing 1 [Gene - OMIM - HGNC]
  • ZFY:zinc finger protein Y-linked [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
Yp11.32-q12
Genomic location:
Preferred name:
GRCh38/hg38 Yp11.32-q12(chrY:10701-57189762)
HGVS:
  • NC_000024.10:g.(?_10701)_(57189762_?)del
  • NC_000024.8:g.(?_701)_(57745301_?)del
  • NC_000024.9:g.(?_10701)_(59335913_?)del
Links:
dbVar: nssv1603977; dbVar: nsv530536
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000175577ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Oct 24, 2012) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
humannot providedyes1not providednot providednot providednot providedclinical 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 1, SCV000175577.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1human1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: Sep 1, 2024