FRMPD1

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

Basic information

Region (hg38): 9:37650954-37746904

Links

ENSG00000070601 ∙ NCBI:22844 ∙ OMIM:616919 ∙ HGNC:29159 ∙ Uniprot:Q5SYB0 ∙ 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 FRMPD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRMPD1 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				2	4	6
missense			92	14	3	109
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	92	16	7

Variants in FRMPD1

This is a list of pathogenic ClinVar variants found in the FRMPD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-37692705-G-A		not specified	Uncertain significance (Jan 19, 2022)
9-37692714-C-G		not specified	Uncertain significance (Apr 19, 2023)
9-37692717-C-T		not specified	Uncertain significance (Jun 22, 2023)
9-37692718-G-A		not specified	Uncertain significance (Feb 23, 2023)
9-37692724-C-G		not specified	Uncertain significance (Oct 01, 2024)
9-37692736-C-T		not specified	Uncertain significance (Aug 21, 2023)
9-37707416-G-T		not specified	Likely benign (Jan 22, 2024)
9-37707417-G-A		not specified	Uncertain significance (Dec 21, 2023)
9-37707451-A-T		not specified	Likely benign (Nov 01, 2021)
9-37707471-C-G		not specified	Uncertain significance (Nov 10, 2024)
9-37707505-C-G		not specified	Uncertain significance (Jul 09, 2021)
9-37707507-C-T		not specified	Uncertain significance (Dec 16, 2023)
9-37708402-G-T		not specified	Uncertain significance (Mar 06, 2023)
9-37708413-G-A		not specified	Uncertain significance (Jun 22, 2021)
9-37708453-A-G		not specified	Uncertain significance (Mar 31, 2023)
9-37711379-T-A		not specified	Uncertain significance (Oct 25, 2023)
9-37711391-C-T		not specified	Uncertain significance (Jun 23, 2023)
9-37719089-C-A		not specified	Uncertain significance (Sep 10, 2024)
9-37719096-G-A		not specified	Uncertain significance (Aug 27, 2024)
9-37719138-C-G		not specified	Uncertain significance (Oct 25, 2022)
9-37729722-T-G			Likely benign (Nov 01, 2024)
9-37729741-C-T		not specified	Uncertain significance (Oct 06, 2024)
9-37729765-G-A		not specified	Uncertain significance (Feb 06, 2024)
9-37729773-G-A		not specified	Uncertain significance (Feb 07, 2023)
9-37729856-A-G			Likely benign (Nov 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRMPD1	protein_coding	protein_coding	ENST00000539465	15	95905

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.19e-12	1.00	125611	0	137	125748	0.000545

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.668	834	890	0.937	0.0000499	10297
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000872	0.000865
Ashkenazi Jewish	0.000899	0.000893
East Asian	0.00109	0.00109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000601	0.000598
Middle Eastern	0.00109	0.00109
South Asian	0.000457	0.000457
Other	0.000326	0.000326

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.375
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0425

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frmpd1

Gene ontology

• Biological process: regulation of G protein-coupled receptor signaling pathway;establishment of protein localization to membrane
• Cellular component: cytosol;cytoskeleton;plasma membrane;cell cortex;protein-containing complex
• Molecular function: protein binding