PRRX2

paired related homeobox 2, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 9:129665647-129722674

Links

ENSG00000167157 ∙ NCBI:51450 ∙ OMIM:604675 ∙ HGNC:21338 ∙ Uniprot:Q99811 ∙ 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 PRRX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRX2 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in PRRX2

This is a list of pathogenic ClinVar variants found in the PRRX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-129665876-C-A		not specified	Uncertain significance (Jun 27, 2022)
9-129665900-C-G		not specified	Uncertain significance (Jan 31, 2024)
9-129665917-C-T		not specified	Uncertain significance (Oct 16, 2024)
9-129665922-C-A		not specified	Uncertain significance (Jul 19, 2022)
9-129665931-C-G		not specified	Uncertain significance (Aug 02, 2021)
9-129666006-G-A		not specified	Uncertain significance (May 24, 2023)
9-129666013-T-G		not specified	Uncertain significance (Nov 12, 2021)
9-129666043-C-T		not specified	Uncertain significance (Nov 16, 2021)
9-129666058-A-G		not specified	Uncertain significance (Nov 16, 2021)
9-129666066-G-C		not specified	Uncertain significance (Jun 17, 2024)
9-129666072-G-A		not specified	Uncertain significance (Dec 12, 2023)
9-129666078-C-T		not specified	Uncertain significance (Oct 05, 2023)
9-129666085-C-G		not specified	Uncertain significance (Aug 14, 2024)
9-129666118-C-T		not specified	Uncertain significance (Feb 06, 2023)
9-129719246-C-T		not specified	Uncertain significance (Aug 12, 2021)
9-129719263-G-T		not specified	Uncertain significance (Jun 07, 2024)
9-129719264-C-T		not specified	Uncertain significance (Jun 07, 2024)
9-129719270-G-T		not specified	Uncertain significance (May 03, 2023)
9-129719278-A-C		not specified	Uncertain significance (Nov 23, 2024)
9-129719288-G-A		not specified	Uncertain significance (Jul 25, 2023)
9-129719300-C-G		not specified	Uncertain significance (Sep 20, 2023)
9-129719342-A-G		not specified	Uncertain significance (Dec 17, 2023)
9-129719343-G-C		not specified	Uncertain significance (Oct 01, 2024)
9-129719371-C-G		not specified	Uncertain significance (Sep 06, 2022)
9-129719395-A-G		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRX2	protein_coding	protein_coding	ENST00000372469	4	56956

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.140	0.787	125696	0	9	125705	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.477	102	116	0.876	0.00000854	1597
Missense in Polyphen		40	58.413	0.68478		501
Synonymous	-0.776	54	47.2	1.14	0.00000336	537
Loss of Function	1.45	2	5.75	0.348	2.45e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.000106	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000552	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the scarless healing of cutaneous wounds during the first two trimesters of development. {ECO:0000269|PubMed:9665387}.

Recessive Scores

• pRec: 0.156

Haploinsufficiency Scores

• pHI: 0.419
• hipred: Y
• hipred_score: 0.521
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prrx2
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal 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); digestive/alimentary phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; vision/eye phenotype

Gene ontology

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