FRMPD1

protein-coding

FERM and PDZ domain containing 1, the group of PDZ domain containing|FERM domain containing

Gene summary

Involved in establishment of protein localization to membrane and regulation of G protein-coupled receptor signaling pathway. Located in cell cortex and plasma membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014907.3

Inheritance

—

ClinVar variants

U:244B:28

Top phenotype

Hepatoblastoma

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr9:37,650,954-37,746,904

External References & Databases

Ensembl (ENSG00000070601)

Transcript & Mutation Effects

hg38 • Region Span ~96.0 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 FRMPD1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 258

not providedTotal: 13

HepatoblastomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014907.3. 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	5 clinvar	4 clinvar	10
missense			243 clinvar	16 clinvar	3 clinvar	262
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	244	21	7	272

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014907.3	RefSeq	NP_055722.2	15	MANE Select
ENST00000377765.8	Ensembl	ENSP00000366995.3	15	MANE Select
NM_001371223.1	RefSeq	NP_001358152.1	15	Standard
NM_001371224.1	RefSeq	NP_001358153.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of G protein-coupled receptor signaling pathway
establishment of protein localization to membrane

Molecular Function

protein binding

Cellular Component

cytosol
cytoskeleton
plasma membrane
cell cortex
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000539465
Coding exons: 15
Length: 95905
Individuals with no LoFs: 125611
Homozygous LoFs: 0
Heterozygous LoFs: 137
Defined: 125748
p: 0.000545

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.668	834	890	0.937	0.0000499	10297
Missense (PolyPhen)		231	274.46	0.84165		3197
Synonymous	-0.0826	367	365	1.01	0.0000221	3218
Loss of Function	3.77	30	62.0	0.483	0.00000335	715

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.00090	0.00089	rare
East Asian	0.0011	0.0011	notable
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00060	0.00060	rare
South Asian	0.00046	0.00046	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Stabilizes membrane-bound GPSM1, and thereby promotes its interaction with GNAI1. {ECO:0000269|PubMed:18566450}.;

Recessive Scores

pRec: 0.0936

Intolerance Scores

LoFtool: 0.855
RVIS EVS: 1.71
RVIS percentile EVS: 96.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0425

Gene Damage Prediction

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