TEX12

testis expressed 12

Basic information

Region (hg38): 11:112167372-112172556

Links

ENSG00000150783 ∙ NCBI:56158 ∙ OMIM:605791 ∙ HGNC:11734 ∙ Uniprot:Q9BXU0 ∙ 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 TEX12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX12 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in TEX12

This is a list of pathogenic ClinVar variants found in the TEX12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-112170449-T-A		not specified	Uncertain significance (Feb 28, 2024)
11-112170465-A-G		not specified	Uncertain significance (Jul 12, 2023)
11-112170494-T-C		not specified	Uncertain significance (Nov 09, 2021)
11-112171830-G-A		not specified	Uncertain significance (Sep 28, 2021)
11-112171854-A-G		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX12	protein_coding	protein_coding	ENST00000280358	4	5188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000457	0.443	125393	0	2	125395	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.296	51	57.3	0.890	0.00000256	803
Missense in Polyphen		10	12.012	0.83252		197
Synonymous	0.0601	21	21.4	0.983	0.00000100	222
Loss of Function	0.0852	5	5.21	0.960	2.18e-7	76

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)	0.00000883	0.00000882
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.402
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.79

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tex12
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: meiotic DNA repair synthesis;synaptonemal complex assembly
• Cellular component: central element