GRCh37/hg19 Yq11.222-11.23(chrY:20608554-28799937)x0 AND Male infertility

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 17, 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:: RCV001090069.1

Allele description [Variation Report for GRCh37/hg19 Yq11.222-11.23(chrY:20608554-28799937)x0]

GRCh37/hg19 Yq11.222-11.23(chrY:20608554-28799937)x0

Genes:

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]
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]
RPS4Y2:ribosomal protein S4 Y-linked 2 [Gene - OMIM - HGNC]
TTTY10:testis-specific transcript, Y-linked 10 [Gene - HGNC]
TTTY13:testis-specific transcript, Y-linked 13 [Gene - HGNC]
TTTY14:testis-specific transcript, Y-linked 14 [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]
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]
TTTY9A:testis-specific transcript, Y-linked 9A [Gene - HGNC]
TTTY9B:testis-specific transcript, Y-linked 9B [Gene - HGNC]

Variant type:

copy number loss

Cytogenetic location:

Yq11.222-11.23

Genomic location:

ChrY: 20608554 - 28799937 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 Yq11.222-11.23(chrY:20608554-28799937)x0

HGVS:

NC_000024.9:g.(?_20608554)_(28799937_?)del

Functional consequence:

No function

Observations:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001132760	Center for Advanced Diagnostics, Brigham and Women's Hospital	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Dec 17, 2019)	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

SCV001132760

Center for Advanced Diagnostics, Brigham and Women's Hospital

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Dec 17, 2019)

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	unknown	yes	1	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 Center for Advanced Diagnostics, Brigham and Women's Hospital, SCV001132760.1

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

Last Updated: Jul 8, 2023

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