DPRX

divergent-paired related homeobox, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:53600777-53637014

Links

ENSG00000204595 ∙ NCBI:503834 ∙ OMIM:611165 ∙ HGNC:32166 ∙ Uniprot:A6NFQ7 ∙ 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 DPRX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPRX 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in DPRX

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

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

Position	Type	Phenotype	Significance	ClinVar
19-53632125-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-53634553-C-A		not specified	Uncertain significance (Oct 19, 2024)
19-53634660-T-C		not specified	Uncertain significance (Aug 20, 2024)
19-53634671-C-T		not specified	Uncertain significance (Sep 30, 2024)
19-53636601-G-T		not specified	Uncertain significance (Apr 12, 2022)
19-53636666-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-53636710-G-A		not specified	Likely benign (Mar 01, 2023)
19-53636741-T-G		not specified	Uncertain significance (Jan 26, 2022)
19-53636777-C-T		not specified	Uncertain significance (Jul 20, 2021)
19-53636815-C-T		not specified	Uncertain significance (Aug 04, 2023)
19-53636842-T-A		not specified	Uncertain significance (Mar 19, 2024)
19-53636846-T-C		not specified	Uncertain significance (Sep 08, 2024)
19-53636878-C-T		Short stature	Pathogenic (Nov 18, 2001)
19-53636929-G-A		not specified	Uncertain significance (Dec 14, 2021)
19-53636935-A-G		not specified	Uncertain significance (Mar 25, 2024)
19-53636977-C-G		not specified	Uncertain significance (Jul 31, 2024)
19-53636978-G-A		not specified	Uncertain significance (Jul 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPRX	protein_coding	protein_coding	ENST00000376650	3	4954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000241	0.0913	125734	0	8	125742	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	81	111	0.732	0.00000590	1253
Missense in Polyphen		13	17.783	0.73105		240
Synonymous	1.75	28	42.5	0.658	0.00000245	370
Loss of Function	-1.25	7	4.22	1.66	2.79e-7	42

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)	0.00000897	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.000133	0.000131
Other	0.000509	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcription factor. {ECO:0000250}.
• Pathway: Preimplantation Embryo (Consensus)

Intolerance Scores

• loftool: 0.555
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.0338
• hipred: N
• hipred_score: 0.146
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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;sequence-specific DNA binding