TEX13B

testis expressed 13B

Basic information

Region (hg38): X:107980864-107982370

Links

ENSG00000170925 ∙ NCBI:56156 ∙ OMIM:300313 ∙ HGNC:11736 ∙ Uniprot:Q9BXU2 ∙ 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 TEX13B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX13B 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in TEX13B

This is a list of pathogenic ClinVar variants found in the TEX13B 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-107981300-C-T		not specified	Uncertain significance (Nov 13, 2024)
X-107981327-C-T		not specified	Uncertain significance (Dec 23, 2022)
X-107981340-C-T		not specified	Uncertain significance (Nov 01, 2022)
X-107981343-C-G		not specified	Uncertain significance (Aug 17, 2021)
X-107981447-G-A		not specified	Uncertain significance (Apr 08, 2024)
X-107981456-G-A		not specified	Uncertain significance (Feb 10, 2022)
X-107981546-G-C		not specified	Uncertain significance (Jan 26, 2023)
X-107981703-T-G		not specified	Uncertain significance (Apr 17, 2024)
X-107981704-C-G		not specified	Uncertain significance (Apr 29, 2024)
X-107981724-C-T		not specified	Uncertain significance (Jan 21, 2025)
X-107981727-G-T		not specified	Uncertain significance (Feb 14, 2023)
X-107981760-T-C		not specified	Uncertain significance (Dec 07, 2024)
X-107981880-C-T		not specified	Uncertain significance (Apr 22, 2024)
X-107981931-G-A		not specified	Uncertain significance (Nov 15, 2023)
X-107981944-C-G		not specified	Uncertain significance (Aug 19, 2024)
X-107981950-G-C		not specified	Uncertain significance (May 23, 2024)
X-107981976-C-T		not specified	Uncertain significance (Mar 13, 2023)
X-107982090-C-G		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX13B	protein_coding	protein_coding	ENST00000302917	2	1507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0111	0.643	124195	476	936	125607	0.00564

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.539	112	129	0.867	0.0000104	2020
Missense in Polyphen		27	26.485	1.0195		493
Synonymous	-0.148	58	56.6	1.02	0.00000500	647
Loss of Function	0.432	3	3.92	0.764	2.49e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0318	0.0258
Ashkenazi Jewish	0.00417	0.00309
East Asian	0.000145	0.000109
Finnish	0.00189	0.00139
European (Non-Finnish)	0.0100	0.00720
Middle Eastern	0.000145	0.000109
South Asian	0.00308	0.00190
Other	0.00723	0.00524

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.261
• rvis_EVS: 0.95
• rvis_percentile_EVS: 89.96

Haploinsufficiency Scores

• pHI: 0.0622
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tex13b