RHPN2

rhophilin Rho GTPase binding protein 2, the group of PDZ domain containing

Basic information

Region (hg38): 19:32978592-33064888

Links

ENSG00000131941 ∙ NCBI:85415 ∙ OMIM:617932 ∙ HGNC:19974 ∙ Uniprot:Q8IUC4 ∙ 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 RHPN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHPN2 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			38	4	4	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	38	5	4

Variants in RHPN2

This is a list of pathogenic ClinVar variants found in the RHPN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-32980015-G-A		not specified	Uncertain significance (May 18, 2023)
19-32980018-T-C		not specified	Uncertain significance (Jul 08, 2022)
19-32980048-T-C		not specified	Uncertain significance (Feb 21, 2024)
19-32980160-T-G		not specified	Uncertain significance (Jan 08, 2024)
19-32980216-G-A		not specified	Uncertain significance (Jun 07, 2024)
19-32980232-C-T		not specified	Uncertain significance (Oct 25, 2022)
19-32990518-G-A		not specified	Uncertain significance (Mar 18, 2024)
19-32990564-C-A		not specified	Uncertain significance (Dec 15, 2022)
19-32990657-G-A		not specified	Uncertain significance (May 04, 2023)
19-32991894-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-32991915-G-A		not specified	Benign (Mar 29, 2016)
19-32991938-C-T		not specified	Uncertain significance (Aug 05, 2023)
19-32993995-C-T			Likely benign (Feb 01, 2023)
19-32994014-A-G		not specified	Uncertain significance (Jan 03, 2024)
19-32996083-C-T		not specified	Likely benign (Feb 28, 2023)
19-32996086-A-C			Benign (Jul 31, 2018)
19-32996094-C-T		not specified	Likely benign (Mar 26, 2024)
19-32996097-G-A		not specified	Uncertain significance (Jan 20, 2023)
19-32996139-A-G		not specified	Uncertain significance (Nov 30, 2022)
19-32996145-C-T		not specified	Uncertain significance (May 26, 2024)
19-32996146-G-A		not specified	Uncertain significance (Sep 17, 2021)
19-32996157-C-A		not specified	Uncertain significance (Nov 18, 2022)
19-32996166-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-32996172-C-T		not specified	Uncertain significance (Sep 27, 2022)
19-32999604-G-C		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHPN2	protein_coding	protein_coding	ENST00000254260	15	86296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.07e-7	0.997	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.315	369	386	0.955	0.0000255	4458
Missense in Polyphen		97	119.31	0.81302		1487
Synonymous	1.27	145	166	0.875	0.0000120	1335
Loss of Function	2.65	17	33.6	0.506	0.00000170	395

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000380	0.000380
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000381	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000381	0.000272
South Asian	0.0000980	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds specifically to GTP-Rho. May function in a Rho pathway to limit stress fiber formation and/or increase the turnover of F-actin structures in the absence of high levels of RhoA activity. {ECO:0000269|PubMed:12221077}.
• Pathway: G13 Signaling Pathway;Signal Transduction;RHO GTPases Activate Rhotekin and Rhophilins;RHO GTPase Effectors;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.744
• rvis_EVS: 0
• rvis_percentile_EVS: 54.07

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.590
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Rhpn2
• Phenotype: normal phenotype

Gene ontology

• Biological process: signal transduction
• Cellular component: cytosol;perinuclear region of cytoplasm