TEX2

protein-coding

testis expressed 2

Gene summary

Predicted to enable lipid binding activity. Predicted to be involved in signal transduction and sphingolipid metabolic process. Predicted to be located in membrane. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001288732.2

Inheritance

—

ClinVar variants

U:161B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr17:64,147,227-64,263,260

External References & Databases

Ensembl (ENSG00000136478)

Transcript & Mutation Effects

hg38 • Region Span ~116.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TEX2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 153

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001288732.2. 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			3 clinvar	1 clinvar		4
missense			153 clinvar	8 clinvar		161
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	161	9	0	170

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001288732.2	RefSeq	NP_001275661.1	11	MANE Select
ENST00000584379.6	Ensembl	ENSP00000463001.1	11	MANE Select
NM_001288733.2	RefSeq	NP_001275662.1	11	Standard
NM_018469.5	RefSeq	NP_060939.3	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

sphingolipid metabolic process
lipid transport
signal transduction

Molecular Function

molecular_function
lipid binding

Cellular Component

endoplasmic reticulum
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000258991
Coding exons: 11
Length: 116075
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.52	510	616	0.828	0.0000338	7415
Missense (PolyPhen)		122	186.05	0.65572		2376
Synonymous	0.0541	250	251	0.996	0.0000156	2257
Loss of Function	4.33	16	48.6	0.330	0.00000303	565

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00055	0.00018	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0801

Intolerance Scores

LoFtool: 0.587
RVIS EVS: -0.95
RVIS percentile EVS: 9.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.506

Gene Damage Prediction

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