TSPY1

protein-coding

testis specific protein Y-linked 1

Gene summary

The protein encoded by this gene is found only in testicular tissue and may be involved in spermatogenesis. Many functional paralogs and pseudogenes of this gene are present in a cluster in humans, but only a single, nonfunctional orthologous gene is found in mouse. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

Previous symbols:

TSPY

MANE transcript

NM_003308.4

Inheritance

—

ClinVar variants

B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrY:9,466,955-9,469,749

External References & Databases

Ensembl (ENSG00000258992)

Transcript & Mutation Effects

hg38 • Region Span ~2.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSPY1 variants in ClinVar

1 Conditions Cataloged

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003308.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense						0
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	0	1	0	1

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003308.4	RefSeq	NP_003299.2	6	MANE Select
ENST00000451548.6	Ensembl	ENSP00000403304.1	6	MANE Select
NM_001197242.2	RefSeq	NP_001184171.1	5	Standard
NM_001320964.2	RefSeq	NP_001307893.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nucleosome assembly
spermatogenesis
gonadal mesoderm development
sex differentiation
cell population proliferation

Molecular Function

molecular_function
protein binding

Cellular Component

cellular_component
nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000451548
Coding exons: 6
Length: 71282
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.105	3	3.55	0.844	5.79e-7	1982
Missense (PolyPhen)		0	0.73506	0		451
Synonymous	0.128	1	1.18	0.850	1.76e-7	595
Loss of Function	0.483	0	0.271	0.00	3.58e-8	155

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in sperm differentiation and proliferation. {ECO:0000269|PubMed:8923009}.;
Disease: DISEASE: Note=TSPY is located in the gonadoblastoma critical region and is preferentially expressed in tumor germ cells of gonadoblastoma specimens. Expression also correlates with testicular seminoma and tumorigenesis of the prostate gland. {ECO:0000269|PubMed:10090875, ECO:0000269|PubMed:10773691, ECO:0000269|PubMed:11173850}.;

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.0711