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GRCh37/hg19 Yq11.21-11.23(chrY:13800703-28799937)x0 AND Male infertility

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 3, 2019
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:
RCV001090084.1

Allele description [Variation Report for GRCh37/hg19 Yq11.21-11.23(chrY:13800703-28799937)x0]

GRCh37/hg19 Yq11.21-11.23(chrY:13800703-28799937)x0

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]
  • 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]
  • FAM197Y10:family with sequence similarity 197 Y-linked member 10 [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]
  • RPS4Y2:ribosomal protein S4 Y-linked 2 [Gene - OMIM - HGNC]
  • TTTY10:testis expressed transcript, Y-linked 10 [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]
  • 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]
  • 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]
  • TTTY9A:testis expressed transcript, Y-linked 9A [Gene - HGNC]
  • TTTY9B:testis expressed transcript, Y-linked 9B [Gene - HGNC]
  • TMSB4Y:thymosin beta 4 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]
Variant type:
copy number loss
Cytogenetic location:
Yq11.21-11.23
Genomic location:
ChrY: 13800703 - 28799937 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 Yq11.21-11.23(chrY:13800703-28799937)x0
HGVS:
NC_000024.9:g.(?_13800703)_(28799937_?)del
Observations:
1

Condition(s)

Name:
Male infertility
Identifiers:
MONDO: MONDO:0005372; MedGen: C0021364; Human Phenotype Ontology: HP:0003251

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001132784Center for Advanced Diagnostics, Brigham and Women's Hospital
criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)		Pathogenic
(Dec 3, 2019) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical 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 Center for Advanced Diagnostics, Brigham and Women's Hospital, SCV001132784.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 1, 2024