TEX19

testis expressed 19

Basic information

Region (hg38): 17:82359246-82363775

Links

ENSG00000182459 ∙ NCBI:400629 ∙ OMIM:615647 ∙ HGNC:33802 ∙ Uniprot:Q8NA77 ∙ 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 TEX19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX19 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			8			8
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	1

Variants in TEX19

This is a list of pathogenic ClinVar variants found in the TEX19 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82362180-G-T		not specified	Uncertain significance (Feb 28, 2023)
17-82362233-G-A		not specified	Uncertain significance (Feb 28, 2023)
17-82362268-G-C		not specified	Uncertain significance (Nov 18, 2022)
17-82362355-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-82362533-A-T		not specified	Uncertain significance (Mar 01, 2023)
17-82362554-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-82362566-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-82362585-TC-T			Benign (Dec 31, 2019)
17-82362608-T-A		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX19	protein_coding	protein_coding	ENST00000333437	1	4530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.321	78	86.4	0.903	0.00000402	1068
Missense in Polyphen		17	21.658	0.78493		284
Synonymous	-0.176	35	33.7	1.04	0.00000165	312
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required during spermatogenesis and placenta development, participating in the repression of retrotransposable elements and prevent their mobilization. Collaborates with the Piwi-interacting RNA (piRNA) pathway, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins. Interacts with Piwi proteins and directly binds piRNAs, a class of 24 to 30 nucleotide RNAs that are generated by a Dicer-independent mechanism and are primarily derived from transposons and other repeated sequence elements. Also during spermatogenesis, promotes, with UBR2, SPO11-dependent recombination foci to accumulate and drive robust homologous chromosome synapsis (By similarity). Interacts with LINE-1 retrotransposon encoded LIRE1, stimulates LIRE1 polyubiquitination, mediated by UBR2, and degradation, inhibiting LINE-1 retranstoposon mobilization (PubMed:28806172). {ECO:0000250|UniProtKB:Q99MV2, ECO:0000269|PubMed:28806172}.

Intolerance Scores

• loftool: 0.430
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.62

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tex19.2
• Phenotype: reproductive system 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); cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: placenta development;reciprocal meiotic recombination;male meiotic nuclear division;spermatogenesis;male gonad development;negative regulation of transposition;cell differentiation
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding;piRNA binding