TPRX1

tetrapeptide repeat homeobox 1, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:47801232-47819051

Links

ENSG00000178928 ∙ NCBI:284355 ∙ OMIM:611166 ∙ HGNC:32174 ∙ Uniprot:Q8N7U7 ∙ 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 TPRX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPRX1 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				6		6
missense			34	6		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	12	0

Variants in TPRX1

This is a list of pathogenic ClinVar variants found in the TPRX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47801791-A-G		not specified	Likely benign (Sep 22, 2023)
19-47801793-C-A		not specified	Uncertain significance (Jan 08, 2024)
19-47801800-C-A		not specified	Uncertain significance (Sep 22, 2023)
19-47801878-C-T		not specified	Uncertain significance (Apr 12, 2022)
19-47801914-G-T		not specified	Uncertain significance (Dec 08, 2023)
19-47801959-G-A		not specified	Uncertain significance (Sep 22, 2023)
19-47801982-G-C		not specified	Uncertain significance (Jun 05, 2023)
19-47801987-C-T		not specified	Uncertain significance (May 11, 2022)
19-47801996-C-T		not specified	Uncertain significance (Jan 20, 2023)
19-47802023-G-T		not specified	Uncertain significance (Apr 09, 2024)
19-47802028-G-A		not specified	Likely benign (Jan 26, 2022)
19-47802136-C-T		not specified	Likely benign (Jul 09, 2021)
19-47802137-G-A		not specified	Uncertain significance (Aug 15, 2023)
19-47802208-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-47802216-A-C		not specified	Uncertain significance (Jan 08, 2024)
19-47802218-T-C		not specified	Uncertain significance (Mar 06, 2023)
19-47802250-G-A		not specified	Uncertain significance (Feb 21, 2024)
19-47802309-C-T			Likely benign (Mar 01, 2023)
19-47802317-A-G		not specified	Likely benign (Jun 24, 2022)
19-47802331-A-T		not specified	Uncertain significance (Jun 24, 2022)
19-47802333-T-C			Likely benign (Oct 01, 2022)
19-47802346-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-47802346-G-C		not specified	Uncertain significance (Apr 04, 2023)
19-47802355-T-A		not specified	Likely benign (Apr 25, 2022)
19-47802357-T-C			Likely benign (Sep 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPRX1	protein_coding	protein_coding	ENST00000322175	2	17809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.359	0.493	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.337	236	222	1.06	0.0000128	2485
Missense in Polyphen		13	13.938	0.9327		156
Synonymous	-0.678	107	98.4	1.09	0.00000560	1002
Loss of Function	0.780	0	0.708	0.00	2.97e-8	11

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Preimplantation Embryo (Consensus)

Intolerance Scores

• loftool: 0.265
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.237
• hipred: N
• hipred_score: 0.112
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0104

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding