TEX2

testis expressed 2

Basic information

Region (hg38): 17:64147226-64263260

Links

ENSG00000136478 ∙ NCBI:55852 ∙ OMIM:619929 ∙ HGNC:30884 ∙ Uniprot:Q8IWB9 ∙ 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 TEX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX2 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			52	5		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	5	0

Variants in TEX2

This is a list of pathogenic ClinVar variants found in the TEX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-64149001-C-A		not specified	Uncertain significance (Oct 26, 2021)
17-64149024-C-T		not specified	Uncertain significance (May 28, 2024)
17-64149082-C-T		not specified	Uncertain significance (Aug 22, 2023)
17-64150884-T-A		not specified	Uncertain significance (May 15, 2024)
17-64150884-T-G		not specified	Uncertain significance (Mar 04, 2024)
17-64152967-G-A		not specified	Uncertain significance (Nov 09, 2023)
17-64154849-C-G		not specified	Uncertain significance (Mar 20, 2023)
17-64160814-T-C		not specified	Uncertain significance (Apr 01, 2024)
17-64160873-T-C		not specified	Uncertain significance (Mar 16, 2022)
17-64160922-C-T		not specified	Uncertain significance (Feb 28, 2024)
17-64171163-G-T		not specified	Uncertain significance (Sep 26, 2023)
17-64171175-T-C		not specified	Uncertain significance (Apr 15, 2024)
17-64177410-C-G		not specified	Uncertain significance (Sep 16, 2021)
17-64188185-G-A		not specified	Uncertain significance (Jan 03, 2024)
17-64188260-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-64188267-G-C		not specified	Uncertain significance (Mar 23, 2023)
17-64188359-G-A		not specified	Uncertain significance (May 14, 2024)
17-64188367-G-A		not specified	Uncertain significance (Dec 26, 2023)
17-64188377-C-T		not specified	Uncertain significance (Sep 16, 2021)
17-64188382-G-A		not specified	Uncertain significance (Jan 31, 2024)
17-64193600-G-A		not specified	Uncertain significance (Jun 06, 2023)
17-64193615-G-T		not specified	Uncertain significance (Jan 09, 2024)
17-64193700-T-C		not specified	Uncertain significance (Nov 28, 2023)
17-64193717-C-T		not specified	Likely benign (Dec 13, 2023)
17-64193751-C-T		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX2	protein_coding	protein_coding	ENST00000258991	11	116075

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000150	1.00	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	510	616	0.828	0.0000338	7415
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000728	0.000358
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.00	0.00
South Asian	0.000170	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0801

Intolerance Scores

• loftool: 0.587
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.38

Haploinsufficiency Scores

• pHI: 0.174
• hipred: Y
• hipred_score: 0.554
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.506

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tex2

Gene ontology

• Biological process: sphingolipid metabolic process;lipid transport;signal transduction
• Cellular component: endoplasmic reticulum;integral component of membrane
• Molecular function: molecular_function;lipid binding