TSPYL2

TSPY like 2

Basic information

Region (hg38): X:53082367-53088540

Links

ENSG00000184205 ∙ NCBI:64061 ∙ OMIM:300564 ∙ HGNC:24358 ∙ Uniprot:Q9H2G4 ∙ 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 TSPYL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPYL2 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				3		3
missense			40	1	1	42
nonsense						0
start loss						0
frameshift			1			1
inframe indel			3	2		5
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	44	7	1

Variants in TSPYL2

This is a list of pathogenic ClinVar variants found in the TSPYL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-53082516-G-C		not specified	Uncertain significance (Mar 18, 2024)
X-53082563-A-G		not specified	Uncertain significance (Jul 09, 2021)
X-53082576-CCCGCCG-C			Likely benign (May 01, 2018)
X-53082576-C-CCCG		not specified	Likely benign (Nov 06, 2015)
X-53082587-C-T		not specified	Uncertain significance (Feb 14, 2023)
X-53082770-G-C		not specified	Uncertain significance (May 23, 2023)
X-53082779-G-T		not specified	Uncertain significance (Jun 07, 2024)
X-53082872-G-T		not specified	Conflicting classifications of pathogenicity (Feb 16, 2023)
X-53082879-C-G		not specified	Uncertain significance (Dec 06, 2023)
X-53082892-T-A		not specified	Uncertain significance (Aug 13, 2021)
X-53082914-G-A		not specified	Uncertain significance (Dec 19, 2023)
X-53083011-A-C			Likely benign (Apr 01, 2023)
X-53083014-GGAGGAT-G			Uncertain significance (Jan 01, 2019)
X-53083056-C-CAGG			Uncertain significance (Apr 01, 2019)
X-53083059-G-C		not specified	Uncertain significance (Dec 16, 2023)
X-53083067-G-A		not specified	Uncertain significance (Apr 25, 2022)
X-53083072-C-T		not specified	Uncertain significance (Mar 28, 2024)
X-53083114-G-A		not specified	Uncertain significance (Jan 19, 2024)
X-53083118-G-T		not specified	Uncertain significance (Jan 23, 2023)
X-53083251-C-T			Likely benign (Feb 01, 2023)
X-53084602-C-T		not specified	Uncertain significance (Feb 23, 2023)
X-53084628-G-A			Benign (Nov 16, 2017)
X-53084760-G-C		not specified	Uncertain significance (May 08, 2024)
X-53084808-G-T		not specified	Uncertain significance (Mar 16, 2022)
X-53084810-C-G		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPYL2	protein_coding	protein_coding	ENST00000375442	7	6174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.874	0.126	125729	6	5	125740	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.330	262	277	0.944	0.0000213	4664
Missense in Polyphen		54	88.548	0.60984		1572
Synonymous	-3.27	157	113	1.39	0.00000943	1245
Loss of Function	3.18	2	15.5	0.129	0.00000109	270

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000149	0.000109
Finnish	0.0000660	0.0000462
European (Non-Finnish)	0.0000786	0.0000527
Middle Eastern	0.000149	0.000109
South Asian	0.000106	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the CASK/TBR1/TSPYL2 transcriptional complex which modulates gene expression in response to neuronal synaptic activity, probably by facilitating nucleosome assembly. May inhibit cell proliferation by inducing p53-dependent CDKN1A expression. {ECO:0000269|PubMed:11395479, ECO:0000269|PubMed:17317670}.
• Pathway: XBP1(S) activates chaperone genes (Consensus)

Recessive Scores

• pRec: 0.277

Intolerance Scores

• loftool: 0.452
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.5

Haploinsufficiency Scores

• pHI: 0.137
• hipred: Y
• hipred_score: 0.519
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspyl2
• Phenotype: cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: nucleosome assembly;cell cycle;negative regulation of DNA replication;regulation of signal transduction;negative regulation of cell growth;IRE1-mediated unfolded protein response;negative regulation of cell cycle;regulation of protein kinase activity
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm
• Molecular function: rDNA binding;protein binding