TSPY1

testis specific protein Y-linked 1

Basic information

Region (hg38): Y:9466955-9469749

Previous symbols: [ "TSPY" ]

Links

ENSG00000258992 ∙ NCBI:7258 ∙ OMIM:480100 ∙ HGNC:12381 ∙ Uniprot:Q01534 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPY1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in TSPY1

This is a list of pathogenic ClinVar variants found in the TSPY1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
Y-9467027-C-T			Likely benign (Jun 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPY1	protein_coding	protein_coding	ENST00000451548	6	71282

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.310	0.500	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.105	3	3.55	0.844	5.79e-7	1982
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.

Haploinsufficiency Scores

• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0711

Gene ontology

• Biological process: nucleosome assembly;spermatogenesis;gonadal mesoderm development;sex differentiation;cell population proliferation;cell differentiation
• Cellular component: cellular_component;nucleus;cytoplasm
• Molecular function: molecular_function;protein binding