PROX2

prospero homeobox 2, the group of PROS class homeoboxes

Basic information

Region (hg38): 14:74852871-74876154

Links

ENSG00000119608 ∙ NCBI:283571 ∙ OMIM:615094 ∙ HGNC:26715 ∙ Uniprot:Q3B8N5 ∙ 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 PROX2 gene.

• not_specified (52 variants)
• not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PROX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001243007.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			51	2	2	55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	2	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PROX2	protein_coding	protein_coding	ENST00000556084	3	10802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.50e-12	0.0163	124592	0	63	124655	0.000253

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.519	176	196	0.896	0.0000104	2380
Missense in Polyphen		50	55.444	0.90181		742
Synonymous	0.590	68	74.5	0.913	0.00000400	719
Loss of Function	-0.554	16	13.8	1.16	7.44e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000433	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000223
Finnish	0.000252	0.000232
European (Non-Finnish)	0.000331	0.000327
Middle Eastern	0.000224	0.000223
South Asian	0.000281	0.000261
Other	0.000358	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription regulator. Does not seem to be essential for embryonic development and postnatal survival (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.123
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0377

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prox2
• Phenotype: normal phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;lymphangiogenesis;positive regulation of transcription by RNA polymerase II;lymphatic endothelial cell differentiation;lens fiber cell morphogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding