TSPYL4

TSPY like 4

Basic information

Region (hg38): 6:116249964-116254075

Links

ENSG00000187189 ∙ NCBI:23270 ∙ OMIM:619586 ∙ HGNC:21559 ∙ Uniprot:Q9UJ04 ∙ 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 TSPYL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPYL4 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			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in TSPYL4

This is a list of pathogenic ClinVar variants found in the TSPYL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116252773-C-G		not specified	Uncertain significance (Dec 06, 2022)
6-116252793-C-T		not specified	Uncertain significance (Feb 12, 2024)
6-116252919-G-T		not specified	Uncertain significance (Dec 08, 2023)
6-116252924-C-T		not specified	Uncertain significance (Jul 19, 2023)
6-116252972-C-T		not specified	Uncertain significance (Aug 16, 2022)
6-116253008-C-G		not specified	Uncertain significance (Apr 10, 2023)
6-116253121-G-C		not specified	Uncertain significance (Jun 06, 2022)
6-116253136-T-G		not specified	Uncertain significance (Jun 05, 2024)
6-116253159-C-G		not specified	Uncertain significance (Jun 07, 2024)
6-116253164-A-G		not specified	Uncertain significance (Jan 16, 2024)
6-116253284-C-T		not specified	Uncertain significance (Sep 17, 2021)
6-116253322-C-T			Likely benign (Mar 01, 2022)
6-116253353-G-T		not specified	Uncertain significance (Oct 12, 2022)
6-116253370-C-G		not specified	Uncertain significance (Apr 12, 2022)
6-116253381-T-C		not specified	Uncertain significance (Aug 12, 2021)
6-116253434-T-C		not specified	Uncertain significance (Dec 26, 2023)
6-116253457-C-A		not specified	Uncertain significance (Dec 02, 2022)
6-116253464-T-C		not specified	Uncertain significance (Dec 17, 2021)
6-116253494-G-A		not specified	Likely benign (Dec 21, 2023)
6-116253546-T-C		not specified	Uncertain significance (Oct 13, 2023)
6-116253632-G-A		not specified	Uncertain significance (Aug 04, 2021)
6-116253641-C-A		not specified	Uncertain significance (Jun 29, 2023)
6-116253642-G-A		not specified	Uncertain significance (Apr 25, 2022)
6-116253690-C-T		not specified	Uncertain significance (Sep 07, 2022)
6-116253708-C-T		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPYL4	protein_coding	protein_coding	ENST00000420283	1	4111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000123	0.620	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.740	206	238	0.865	0.0000124	2663
Missense in Polyphen		63	86.245	0.73047		1021
Synonymous	-0.644	97	89.3	1.09	0.00000426	842
Loss of Function	0.868	9	12.3	0.733	7.63e-7	127

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

Intolerance Scores

• loftool: 0.726
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.211
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspyl4

Gene ontology

• Biological process: nucleosome assembly
• Cellular component: nucleus
• Molecular function: protein binding