TEX11

testis expressed 11

Basic information

Region (hg38): X:70528939-70908711

Links

ENSG00000120498 ∙ ∙ OMIM:300311 ∙ HGNC:11733 ∙ Uniprot:Q8IYF3 ∙ 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, X-linked, 2 (Moderate), mode of inheritance: XL
• spermatogenic failure, X-linked, 2 (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure, X-linked 2	XL	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	Genitourinary	25970010

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TEX11 gene.

• Inborn genetic diseases (19 variants)
• not provided (18 variants)
• Non-obstructive azoospermia (7 variants)
• not specified (3 variants)
• Spermatogenic failure, X-linked, 2 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX11 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	2
missense	1		20	4	3	28
nonsense	1					1
start loss						0
frameshift	3					3
inframe indel						0
splice donor/acceptor (+/-2bp)	2					2
splice region				3	1	4
non coding						0
Total	7	0	20	5	4

Variants in TEX11

This is a list of pathogenic ClinVar variants found in the TEX11 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-70529119-A-C		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
X-70529120-T-C		Inborn genetic diseases	Uncertain significance (Dec 27, 2022)
X-70529854-T-C			Uncertain significance (Sep 01, 2023)
X-70529906-C-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
X-70529946-G-A			Likely benign (Feb 01, 2024)
X-70529952-C-A		Non-obstructive azoospermia	Pathogenic (-)
X-70552150-A-C			Benign (Dec 14, 2018)
X-70552150-A-G		TEX11-related disorder	Benign (Mar 27, 2019)
X-70552182-G-C			Uncertain significance (Feb 01, 2020)
X-70552198-C-T		TEX11-related disorder	Likely benign (Mar 06, 2019)
X-70552201-C-T		TEX11-related disorder	Likely benign (Apr 01, 2019)
X-70553312-T-C			Likely benign (Mar 01, 2024)
X-70553329-T-A		Inborn genetic diseases	Uncertain significance (Aug 15, 2023)
X-70553405-A-G		Inborn genetic diseases	Uncertain significance (Oct 27, 2022)
X-70553406-T-C		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
X-70554643-G-T			Likely benign (May 07, 2018)
X-70554698-A-G		not specified	Benign/Likely benign (May 04, 2022)
X-70554699-C-A		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
X-70605421-C-T		Spermatogenic failure, X-linked, 2 • not specified	Conflicting classifications of pathogenicity (Feb 21, 2024)
X-70609156-G-C		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
X-70610514-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 27, 2023)
X-70623948-A-C		Non-obstructive azoospermia	Pathogenic (-)
X-70629626-G-C			Likely benign (Nov 01, 2022)
X-70629688-A-G		Inborn genetic diseases	Uncertain significance (Oct 16, 2023)
X-70629708-T-G		Inborn genetic diseases	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX11	protein_coding	protein_coding	ENST00000395889	29	379792

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000171	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	204	291	0.701	0.0000205	6233
Missense in Polyphen		21	61.514	0.34138		1438
Synonymous	-1.69	122	100	1.21	0.00000724	1631
Loss of Function	5.64	0	37.1	0.00	0.00000262	745

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

• Function: FUNCTION: Regulator of crossing-over during meiosis. Involved in initiation and/or maintenance of chromosome synapsis and formation of crossovers. {ECO:0000250|UniProtKB:Q14AT2}.

Recessive Scores

• pRec: 0.0813

Intolerance Scores

• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.466
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tex11
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: resolution of meiotic recombination intermediates;meiotic gene conversion;male meiosis chromosome segregation;synaptonemal complex assembly;reciprocal meiotic recombination;male gonad development;fertilization;negative regulation of apoptotic process;chiasma assembly
• Cellular component: synaptonemal complex;central element
• Molecular function: protein binding