TSPYL1

TSPY like 1

Basic information

Region (hg38): 6:116267760-116279930

Previous symbols: [ "TSPYL" ]

Links

ENSG00000189241 ∙ NCBI:7259 ∙ OMIM:604714 ∙ HGNC:12382 ∙ Uniprot:Q9H0U9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• sudden infant death-dysgenesis of the testes syndrome (Supportive), mode of inheritance: AR
• sudden infant death-dysgenesis of the testes syndrome (Moderate), mode of inheritance: AR
• sudden infant death-dysgenesis of the testes syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Sudden infant death with dysgenesis of the testes syndrome; 46, XY disorder of sex development	AR	General	In Sudden infant death with dysgenesis of the testes syndrome, death has been described during inpatient cardiorespiratory monitoring; In 46, XY disorder of sexual development, individuals may have the potential for gonadal tumors; Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary; Neurologic	15273283; 19463995

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPYL1 gene.

• Inborn_genetic_diseases (52 variants)
• not_provided (26 variants)
• Sudden_infant_death-dysgenesis_of_the_testes_syndrome (8 variants)
• TSPYL1-related_disorder (4 variants)
• not_specified (2 variants)
• DSE-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPYL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003309.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	13	1	15
missense			53	6	2	61
nonsense			1			1
start loss						0
frameshift	1	2	1			4
splice donor/acceptor (+/-2bp)						0
Total	1	2	56	19	3

Highest pathogenic variant AF is 0.000032836124

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPYL1	protein_coding	protein_coding	ENST00000368608	1	3326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.62e-7	0.438	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.425	230	249	0.924	0.0000133	2824
Missense in Polyphen		30	58.195	0.51551		726
Synonymous	-3.34	140	97.9	1.43	0.00000511	891
Loss of Function	0.694	11	13.8	0.798	7.62e-7	156

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

• Pathway: Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways (Consensus)

Recessive Scores

• pRec: 0.0960

Intolerance Scores

• loftool: 0.476
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.14

Haploinsufficiency Scores

• pHI: 0.0968
• hipred: N
• hipred_score: 0.278
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.779

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tspyl1

Gene ontology

• Biological process: nucleosome assembly;biological_process
• Cellular component: nucleus;nucleolus
• Molecular function: enzyme binding