TEX9

testis expressed 9

Basic information

Region (hg38): 15:56243971-56445997

Links

ENSG00000151575 ∙ NCBI:374618 ∙ ∙ HGNC:29585 ∙ Uniprot:Q8N6V9 ∙ 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 TEX9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX9 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		3	23	5	2	33
Total	0	3	40	5	2

Variants in TEX9

This is a list of pathogenic ClinVar variants found in the TEX9 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-56365460-C-G		not specified	Uncertain significance (Mar 17, 2023)
15-56373464-C-G		not specified	Uncertain significance (Dec 14, 2021)
15-56383958-C-T		not specified	Uncertain significance (Oct 06, 2023)
15-56383971-G-T		not specified	Uncertain significance (Jun 07, 2024)
15-56383973-T-C		not specified	Uncertain significance (Mar 20, 2023)
15-56383980-C-G		not specified	Uncertain significance (Sep 20, 2023)
15-56388504-T-G		not specified	Uncertain significance (Apr 26, 2024)
15-56388512-G-A		not specified	Uncertain significance (Jan 10, 2022)
15-56389359-C-A		not specified	Uncertain significance (Feb 10, 2022)
15-56391262-G-A		not specified	Uncertain significance (Jan 09, 2023)
15-56391280-G-A		not specified	Uncertain significance (Dec 20, 2023)
15-56391344-G-A		not specified	Uncertain significance (May 01, 2022)
15-56391395-G-A		not specified	Uncertain significance (Oct 05, 2023)
15-56391406-G-C		not specified	Uncertain significance (Jan 03, 2022)
15-56412409-G-T		not specified	Uncertain significance (Oct 25, 2022)
15-56427605-G-T		not specified	Uncertain significance (Feb 22, 2023)
15-56427634-T-G		not specified	Uncertain significance (Jun 17, 2024)
15-56427732-G-C		not specified	Uncertain significance (Feb 23, 2023)
15-56428388-A-G		not specified	Uncertain significance (Mar 14, 2023)
15-56428412-T-A		not specified	Uncertain significance (Dec 14, 2023)
15-56429102-C-A		MNS1-related disorder	Benign (Sep 25, 2020)
15-56429168-A-T		not specified	Uncertain significance (Dec 07, 2023)
15-56429175-C-T		not specified	Uncertain significance (Jan 04, 2022)
15-56429184-T-A			Uncertain significance (Oct 30, 2019)
15-56429190-C-T		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX9	protein_coding	protein_coding	ENST00000352903	12	201989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.42e-22	0.000224	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.746	218	189	1.15	0.00000886	2571
Missense in Polyphen		49	47.016	1.0422		681
Synonymous	-0.266	71	68.2	1.04	0.00000339	661
Loss of Function	-0.760	30	25.8	1.16	0.00000127	337

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00108
Ashkenazi Jewish	0.00	0.00
East Asian	0.000950	0.000925
Finnish	0.0000509	0.0000462
European (Non-Finnish)	0.000268	0.000264
Middle Eastern	0.000950	0.000925
South Asian	0.000786	0.000719
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0809

Intolerance Scores

• loftool: 0.423
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

• pHI: 0.0592
• hipred: N
• hipred_score: 0.167
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tex9

Gene ontology

• Molecular function: protein binding