TSPYL6

TSPY like 6

Basic information

Region (hg38): 2:54253177-54256229

Links

ENSG00000178021 ∙ NCBI:388951 ∙ ∙ HGNC:14521 ∙ Uniprot:Q8N831 ∙ 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 TSPYL6 gene.

• Inborn genetic diseases (20 variants)
• not provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPYL6 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				2	4	6
missense			18	2	5	25
nonsense						0
start loss				1	1	2
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	5	11

Variants in TSPYL6

This is a list of pathogenic ClinVar variants found in the TSPYL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-54254983-G-A		not specified	Uncertain significance (Apr 17, 2023)
2-54255130-T-C		not specified	Uncertain significance (Sep 14, 2023)
2-54255157-C-T		not specified	Likely benign (Feb 28, 2023)
2-54255162-C-A		not specified	Uncertain significance (Oct 14, 2023)
2-54255197-C-A		not specified	Uncertain significance (Feb 05, 2024)
2-54255254-T-C		not specified	Uncertain significance (Nov 13, 2023)
2-54255267-C-G		not specified	Uncertain significance (Jul 05, 2022)
2-54255301-T-A		not specified	Uncertain significance (Feb 13, 2024)
2-54255309-T-G		not specified	Uncertain significance (Jul 26, 2022)
2-54255336-C-G		not specified	Uncertain significance (Jan 03, 2024)
2-54255357-C-G		not specified	Uncertain significance (Sep 26, 2023)
2-54255518-G-C		not specified	Uncertain significance (Feb 17, 2022)
2-54255566-GGGGCCC-G			Benign (Dec 31, 2019)
2-54255569-G-A		not specified	Uncertain significance (Jun 28, 2023)
2-54255574-G-A		not specified	Uncertain significance (Aug 21, 2023)
2-54255600-G-C		not specified	Likely benign (Feb 23, 2023)
2-54255616-G-A		not specified	Uncertain significance (Apr 05, 2023)
2-54255705-G-A			Benign (Dec 31, 2019)
2-54255724-G-A		not specified	Uncertain significance (Jun 26, 2023)
2-54255744-C-A		not specified	Uncertain significance (Nov 15, 2021)
2-54255751-G-C		not specified	Uncertain significance (Jul 14, 2023)
2-54255776-C-T		not specified	Uncertain significance (Sep 27, 2021)
2-54255794-T-C		not specified	Uncertain significance (Dec 01, 2022)
2-54255805-G-A			Benign (Feb 20, 2018)
2-54255840-C-A			Likely benign (Sep 07, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPYL6	protein_coding	protein_coding	ENST00000317802	1	3095

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.71	326	250	1.30	0.0000152	2686
Missense in Polyphen		33	45.58	0.724		599
Synonymous	-1.02	124	110	1.12	0.00000778	836
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.323
• rvis_EVS: 1.16
• rvis_percentile_EVS: 92.59

Haploinsufficiency Scores

• pHI: 0.0466
• hipred: N
• hipred_score: 0.158

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

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

Gene ontology

• Biological process: nucleosome assembly
• Cellular component: nucleus