TSBP1

testis expressed basic protein 1

Basic information

Region (hg38): 6:32288525-32371907

Previous symbols: [ "C6orf10" ]

Links

ENSG00000204296 ∙ NCBI:10665 ∙ OMIM:618151 ∙ HGNC:13922 ∙ Uniprot:Q5SRN2 ∙ 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 TSBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSBP1 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

Variants in TSBP1

This is a list of pathogenic ClinVar variants found in the TSBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32293553-C-T		not specified	Uncertain significance (Sep 17, 2021)
6-32293734-C-T		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSBP1	protein_coding	protein_coding	ENST00000447241	23	83382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-16	0.0444	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	208	278	0.748	0.0000130	3615
Missense in Polyphen		67	91.871	0.72928		1376
Synonymous	1.89	70	93.2	0.751	0.00000449	1021
Loss of Function	0.738	27	31.5	0.858	0.00000177	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00149	0.00144
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000193	0.000185
Middle Eastern	0.0000547	0.0000544
South Asian	0.000203	0.000196
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0744

Intolerance Scores

• rvis_EVS: 4.27
• rvis_percentile_EVS: 99.73

Haploinsufficiency Scores

• pHI: 0.0759
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: BC051142
• Phenotype: normal phenotype

Gene ontology

• Cellular component: nucleus;integral component of membrane