TEX15

testis expressed 15, meiosis and synapsis associated

Basic information

Region (hg38): 8:30831544-30913008

Links

ENSG00000133863 ∙ NCBI:56154 ∙ OMIM:605795 ∙ HGNC:11738 ∙ Uniprot:Q9BXT5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Supportive), mode of inheritance: AD
• spermatogenic failure 25 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 25	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Endocrine; Genitourinary	26199321; 28303806; 28355598

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TEX15 gene.

• not provided (3 variants)
• Spermatogenic failure 25 (2 variants)
• Non-obstructive azoospermia (1 variants)
• Oligosynaptic infertility (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX15 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				19	10	29
missense		1	165	33	15	214
nonsense	3	2	1			6
start loss						0
frameshift	3	3	2			8
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1	1	3
non coding			1			1
Total	6	6	169	52	25

Highest pathogenic variant AF is 0.000197

Variants in TEX15

This is a list of pathogenic ClinVar variants found in the TEX15 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-30836810-C-T			Conflicting classifications of pathogenicity (May 01, 2024)
8-30836822-T-C			Benign/Likely benign (Nov 01, 2024)
8-30836836-G-A		Non-obstructive azoospermia	Uncertain significance (Mar 16, 2022)
8-30836848-A-G		not specified	Uncertain significance (Nov 15, 2021)
8-30836859-G-C		not specified	Uncertain significance (Dec 26, 2023)
8-30836916-G-A		TEX15-related disorder	Benign (Jul 13, 2018)
8-30836927-T-G		not specified	Uncertain significance (Mar 14, 2023)
8-30836928-T-A		not specified	Uncertain significance (Mar 14, 2023)
8-30836946-T-C		not specified	Uncertain significance (Jan 10, 2022)
8-30836960-G-A			Likely benign (Aug 01, 2022)
8-30836961-C-A		not specified	Uncertain significance (Jan 19, 2022)
8-30836991-G-A		not specified	Uncertain significance (Apr 12, 2022)
8-30837009-A-C		not specified	Uncertain significance (Mar 29, 2022)
8-30837024-G-A		not specified	Uncertain significance (May 30, 2024)
8-30837028-C-G		not specified	Uncertain significance (Jan 19, 2024)
8-30837061-C-T		Non-obstructive azoospermia	Conflicting classifications of pathogenicity (Aug 01, 2023)
8-30837091-T-C		not specified	Uncertain significance (Jun 02, 2024)
8-30837102-T-C		not specified	Uncertain significance (Dec 16, 2023)
8-30837140-C-G		not specified	Likely benign (Jan 04, 2022)
8-30837159-G-C		not specified	Uncertain significance (Nov 08, 2022)
8-30837165-G-A		not specified	Uncertain significance (Mar 05, 2024)
8-30837213-C-A		not specified	Uncertain significance (Dec 05, 2022)
8-30837229-G-A		not specified	Uncertain significance (Feb 14, 2023)
8-30837259-T-C		not specified	Uncertain significance (Oct 26, 2021)
8-30837357-T-C		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX15	protein_coding	protein_coding	ENST00000256246	4	59063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.99e-25	0.998	123769	0	3	123772	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.15	1483	1.36e+3	1.09	0.0000648	18595
Missense in Polyphen		243	269.22	0.90262		4023
Synonymous	-1.47	551	509	1.08	0.0000265	5069
Loss of Function	3.27	53	85.6	0.619	0.00000416	1318

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)	0.00000974	0.00000887
Middle Eastern	0.00	0.00
South Asian	0.0000779	0.0000684
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required during spermatogenesis for normal chromosome synapsis and meiotic recombination in germ cells. Necessary for formation of DMC1 and RAD51 foci on meiotic chromosomes, suggesting a specific role in DNA double-stranded break repair. {ECO:0000250|UniProtKB:F8VPN2}.

Recessive Scores

• pRec: 0.0693

Intolerance Scores

• loftool: 0.968
• rvis_EVS: 2.71
• rvis_percentile_EVS: 98.91

Haploinsufficiency Scores

• pHI: 0.0556
• hipred: N
• hipred_score: 0.173

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.125

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tex15
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; reproductive system phenotype

Gene ontology

• Biological process: DNA repair;synapsis;male meiotic nuclear division;spermatogenesis;regulation of double-strand break repair via homologous recombination;cell differentiation
• Cellular component: nucleus;cytoplasm