TSPYL1

TSPY like 1

Basic information

Region (hg38): 6:116267759-116279930

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.

• not provided (24 variants)
• Inborn genetic diseases (14 variants)
• Sudden infant death-dysgenesis of the testes syndrome (3 variants)
• not specified (2 variants)
• Ehlers-Danlos syndrome, musculocontractural type 2 (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.

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	8		9
missense			19	3	5	27
nonsense			1			1
start loss						0
frameshift		2				2
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	21	12	6

Highest pathogenic variant AF is 0.00000658

Variants in TSPYL1

This is a list of pathogenic ClinVar variants found in the TSPYL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116278562-C-T			Likely benign (Jun 08, 2018)
6-116278567-G-A			Likely benign (Oct 13, 2022)
6-116278696-T-C		not specified	Benign (Jan 04, 2024)
6-116278715-G-A			Likely benign (Jul 22, 2021)
6-116278733-G-T		not specified • TSPYL1-related disorder	Likely benign (Jan 22, 2024)
6-116278748-A-G		TSPYL1-related disorder	Likely benign (Jul 12, 2019)
6-116278764-A-G		Inborn genetic diseases	Uncertain significance (Apr 01, 2022)
6-116278772-A-G			Likely benign (Sep 03, 2021)
6-116278911-A-G		Sudden infant death-dysgenesis of the testes syndrome	Uncertain significance (-)
6-116278928-T-C			Likely benign (Dec 19, 2022)
6-116278942-C-A		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
6-116278948-C-T		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
6-116279003-C-T			Likely benign (Nov 01, 2022)
6-116279076-T-C		Inborn genetic diseases	Uncertain significance (Jan 16, 2024)
6-116279104-TCA-T		Sudden infant death-dysgenesis of the testes syndrome	Pathogenic/Likely pathogenic (May 14, 2020)
6-116279184-T-G		Inborn genetic diseases	Uncertain significance (Sep 23, 2023)
6-116279191-C-A		Inborn genetic diseases	Uncertain significance (Nov 04, 2022)
6-116279212-C-T		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
6-116279230-C-T		Inborn genetic diseases	Uncertain significance (Jul 19, 2022)
6-116279246-C-A		Inborn genetic diseases	Uncertain significance (Apr 08, 2022)
6-116279251-C-A			Uncertain significance (Aug 24, 2022)
6-116279256-ACCT-A			Likely benign (Apr 03, 2023)
6-116279265-T-G		Inborn genetic diseases	Uncertain significance (Jun 11, 2021)
6-116279290-C-T			Benign (Jan 29, 2024)
6-116279302-T-TCAC		Ehlers-Danlos syndrome, musculocontractural type 2	Benign (Jan 31, 2024)

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