TEX10

testis expressed 10, the group of Armadillo like helical domain containing|Large ribosomal subunit biogenesis complex

Basic information

Region (hg38): 9:100302077-100352942

Links

ENSG00000136891 ∙ NCBI:54881 ∙ OMIM:616717 ∙ HGNC:25988 ∙ Uniprot:Q9NXF1 ∙ 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 TEX10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX10 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			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	0	0

Variants in TEX10

This is a list of pathogenic ClinVar variants found in the TEX10 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-100302237-A-G		not specified	Uncertain significance (Mar 16, 2022)
9-100302304-T-C		not specified	Uncertain significance (Dec 21, 2022)
9-100303682-G-A		not specified	Uncertain significance (Dec 20, 2023)
9-100303751-C-T		not specified	Uncertain significance (Oct 10, 2023)
9-100303760-T-C		not specified	Uncertain significance (Feb 10, 2022)
9-100303781-T-C		not specified	Uncertain significance (Feb 16, 2023)
9-100308536-G-C		not specified	Uncertain significance (Jan 18, 2022)
9-100310313-T-C		not specified	Uncertain significance (Sep 27, 2022)
9-100310376-C-T		not specified	Uncertain significance (Apr 12, 2022)
9-100320356-C-T		not specified	Uncertain significance (May 25, 2022)
9-100321720-A-T		not specified	Uncertain significance (Dec 06, 2022)
9-100326308-T-C		not specified	Uncertain significance (Jun 17, 2024)
9-100326335-A-C		not specified	Uncertain significance (Nov 30, 2021)
9-100326338-C-T		not specified	Uncertain significance (May 26, 2024)
9-100326450-G-A		not specified	Uncertain significance (Mar 25, 2024)
9-100327816-C-T		not specified	Uncertain significance (Aug 08, 2023)
9-100327862-T-C		not specified	Uncertain significance (May 01, 2024)
9-100327940-G-A		not specified	Uncertain significance (Jan 30, 2024)
9-100329177-T-G		not specified	Uncertain significance (Oct 29, 2021)
9-100329200-A-G		not specified	Uncertain significance (Oct 04, 2022)
9-100329269-G-A		not specified	Uncertain significance (Jun 03, 2022)
9-100329981-T-C		not specified	Uncertain significance (Jun 10, 2022)
9-100330005-G-C		not specified	Uncertain significance (Oct 13, 2023)
9-100330155-G-A		not specified	Uncertain significance (Jun 03, 2022)
9-100340317-C-T		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX10	protein_coding	protein_coding	ENST00000374902	14	50863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000470	125735	0	8	125743	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	384	479	0.802	0.0000240	6057
Missense in Polyphen		79	120.73	0.65438		1634
Synonymous	1.62	149	176	0.845	0.00000845	1835
Loss of Function	5.99	3	47.6	0.0630	0.00000278	522

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000918	0.0000918
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000362	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTOP, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes (PubMed:22872859). Component of the PELP1 complex involved in the nucleolar steps of 28S rRNA maturation and the subsequent nucleoplasmic transit of the pre-60S ribosomal subunit (PubMed:21326211). {ECO:0000269|PubMed:21326211, ECO:0000269|PubMed:22872859}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.0464
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.67

Haploinsufficiency Scores

• pHI: 0.534
• hipred: Y
• hipred_score: 0.853
• ghis: 0.641

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.671

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tex10
• Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleoplasm;nucleolus;cytoplasm;MLL1 complex;Rix1 complex
• Molecular function: protein binding