PROX2

prospero homeobox 2, the group of PROS class homeoboxes

Basic information

Region (hg38): 14:74852870-74876154

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.

• Inborn genetic diseases (16 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.

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					1	1
missense			16	1	2	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	3

Variants in PROX2

This is a list of pathogenic ClinVar variants found in the PROX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-74855140-G-T		not specified	Uncertain significance (Jan 20, 2023)
14-74855158-A-G		not specified	Uncertain significance (Sep 26, 2022)
14-74855164-C-G		not specified	Uncertain significance (Jan 24, 2024)
14-74855202-A-G		not specified	Uncertain significance (Dec 07, 2023)
14-74855277-G-A		not specified	Uncertain significance (Feb 21, 2024)
14-74855293-A-C		not specified	Uncertain significance (Apr 28, 2022)
14-74856935-A-G		not specified	Uncertain significance (Nov 14, 2023)
14-74856974-G-T		not specified	Uncertain significance (Feb 15, 2023)
14-74856989-G-A		not specified	Uncertain significance (Jun 11, 2021)
14-74862615-T-C			Benign (Jun 01, 2022)
14-74863148-C-G		not specified	Uncertain significance (Oct 10, 2023)
14-74863153-T-C		not specified	Uncertain significance (Nov 18, 2022)
14-74863185-G-C		not specified	Uncertain significance (Jan 04, 2022)
14-74863188-G-A		not specified	Uncertain significance (Oct 04, 2022)
14-74863240-C-T		not specified	Uncertain significance (Aug 17, 2021)
14-74863284-C-T		not specified	Uncertain significance (Jan 23, 2024)
14-74863332-G-A		not specified	Uncertain significance (Oct 25, 2022)
14-74863363-C-T		not specified	Uncertain significance (Nov 14, 2023)
14-74863437-C-T		not specified	Uncertain significance (Mar 31, 2023)
14-74863444-G-A		not specified	Uncertain significance (Sep 17, 2021)
14-74863446-G-C		not specified	Uncertain significance (Jan 02, 2024)
14-74863455-T-C			Benign (May 18, 2018)
14-74863486-G-T		not specified	Uncertain significance (May 24, 2023)
14-74863502-C-T			Benign (May 18, 2018)
14-74863510-G-A		not specified	Uncertain significance (Oct 13, 2023)

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