TEX11

protein-coding

testis expressed 11

Gene summary

This gene is X-linked and is expressed in only male germ cells. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_031276.3

Inheritance

AD, XL

ClinVar variants

P:13U:129B:35

Top phenotype

Spermatogenic failure, X-linked 2

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:70,528,940-70,908,711

External References & Databases

Ensembl (ENSG00000120498)

Transcript & Mutation Effects

hg38 • Region Span ~379.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

male infertility with azoospermia or oligozoospermia due to single gene mutationSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018393

Submitter: Orphanet

spermatogenic failure, X-linked, 2STRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010647

Submitter: Labcorp Genetics (formerly Invitae)

spermatogenic failure, X-linked, 2MODERATE

Inheritance Pattern: XL

Disease ID:MONDO:0010647

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Spermatogenic failure, X-linked 2XL

Manifestation: Genitourinary

Intervention: General

Rationale: 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

Refs: 25970010

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TEX11 variants in ClinVar

7 Conditions Cataloged

Inborn genetic diseasesTotal: 80

not providedTotal: 22

not specifiedTotal: 14

TEX11-related disorderTotal: 9

Non-obstructive azoospermiaTotal: 7

Male infertilityTotal: 6

Spermatogenic failure, X-linked, 2Total: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031276.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	10 clinvar	2 clinvar	16
missense	1 clinvar		106 clinvar	20 clinvar	3 clinvar	130
nonsense	3 clinvar		5 clinvar			8
start loss						0
frameshift	4 clinvar	1 clinvar				5
splice donor/acceptor (+/-2bp)	4 clinvar		14 clinvar			18
Total	12	1	129	30	5	177

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031276.3	RefSeq	NP_112566.2	29	MANE Select
ENST00000374333.7	Ensembl	ENSP00000363453.2	29	MANE Select
NM_001003811.2	RefSeq	NP_001003811.1	29	Standard
ENST00000344304.3	Ensembl	ENSP00000340995.3	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

resolution of meiotic recombination intermediates
meiotic gene conversion
male meiosis chromosome segregation
synaptonemal complex assembly
reciprocal meiotic recombination

Molecular Function

protein binding

Cellular Component

synaptonemal complex
central element

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395889
Coding exons: 29
Length: 379792
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.81	204	291	0.701	0.0000205	6233
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.149

Gene Damage Prediction

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