RHPN1

protein-coding

rhophilin Rho GTPase binding protein 1, the group of PDZ domain containing

Gene summary

Predicted to be involved in negative regulation of stress fiber assembly. Predicted to act upstream of or within several processes, including focal adhesion assembly; glomerular filtration; and renal albumin absorption. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_052924.3

Inheritance

—

ClinVar variants

U:157B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr8:143,368,876-143,384,221

External References & Databases

Ensembl (ENSG00000158106)

Transcript & Mutation Effects

hg38 • Region Span ~15.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RHPN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 158

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052924.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			148 clinvar	13 clinvar		161
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	157	15	0	172

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 102 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052924.3	RefSeq	NP_443156.2	15	MANE Select
ENST00000289013.11	Ensembl	ENSP00000289013.6	15	MANE Select
ENST00000715591.1	Ensembl	ENSP00000520485.1	13	Standard
ENST00000715591.2	Ensembl	ENSP00000520485.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation
Signal Transduction
RHO GTPases Activate Rhotekin and Rhophilins
RHO GTPase Effectors
Signaling by Rho GTPases

Biological Process

signal transduction

Molecular Function

protein binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000289013
Coding exons: 15
Length: 15334
Individuals with no LoFs: 124400
Homozygous LoFs: 0
Heterozygous LoFs: 97
Defined: 124497
p: 0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.407	388	411	0.944	0.0000279	4183
Missense (PolyPhen)		113	140.3	0.80544		1583
Synonymous	-0.964	208	191	1.09	0.0000139	1409
Loss of Function	1.08	22	28.2	0.780	0.00000138	317

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00019	rare
Latino/Admixed American	0.00025	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00062	0.00061	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00064	0.00055	rare
South Asian	0.00034	0.00033	rare
Other	0.00056	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has no enzymatic activity. May serve as a target for Rho, and interact with some cytoskeletal component upon Rho binding or relay a Rho signal to other molecules. {ECO:0000250|UniProtKB:Q61085}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.818
RVIS EVS: -0.53
RVIS percentile EVS: 20.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.795

Gene Damage Prediction

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