FRMPD2

FERM and PDZ domain containing 2, the group of FERM domain containing|PDZ domain containing

Basic information

Region (hg38): 10:48153087-48274696

Previous symbols: [ "PDZD5C", "PDZK5C" ]

Links

ENSG00000170324 ∙ NCBI:143162 ∙ OMIM:613323 ∙ HGNC:28572 ∙ Uniprot:Q68DX3 ∙ 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 FRMPD2 gene.

• Inborn genetic diseases (49 variants)
• not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRMPD2 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				5		5
missense			47	6	2	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	11	2

Variants in FRMPD2

This is a list of pathogenic ClinVar variants found in the FRMPD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-48157342-G-A		not specified	Uncertain significance (Oct 05, 2022)
10-48163340-A-C		not specified	Likely benign (Dec 13, 2023)
10-48163466-G-A		not specified	Uncertain significance (Nov 17, 2023)
10-48163542-G-A		not specified	Uncertain significance (Feb 27, 2023)
10-48163550-C-A		not specified	Uncertain significance (Jan 23, 2023)
10-48163574-C-T		not specified	Uncertain significance (Oct 29, 2021)
10-48163608-G-T		not specified	Uncertain significance (Jan 26, 2023)
10-48163621-G-A			Likely benign (Jun 01, 2022)
10-48171047-C-T		not specified	Uncertain significance (Dec 08, 2023)
10-48171068-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-48171085-G-A		not specified	Uncertain significance (May 13, 2022)
10-48172969-G-A		not specified	Uncertain significance (Jan 19, 2022)
10-48174919-C-T		not specified	Uncertain significance (Feb 23, 2023)
10-48175891-T-G		not specified	Uncertain significance (Jul 05, 2023)
10-48178064-G-T		not specified	Uncertain significance (Apr 04, 2023)
10-48178073-C-A		not specified	Uncertain significance (Dec 13, 2023)
10-48178108-G-A			Benign (Jun 08, 2018)
10-48178136-A-C		not specified	Uncertain significance (Nov 08, 2022)
10-48178141-G-T			Likely benign (Mar 01, 2023)
10-48180942-T-C		not specified	Uncertain significance (Mar 06, 2023)
10-48181002-C-T		not specified	Uncertain significance (Jan 17, 2024)
10-48184610-T-C		not specified	Uncertain significance (Dec 14, 2023)
10-48184619-C-T		not specified	Uncertain significance (May 30, 2023)
10-48184672-T-C		not specified	Uncertain significance (Sep 27, 2022)
10-48184809-C-G		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRMPD2	protein_coding	protein_coding	ENST00000374201	29	118341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.51e-32	0.000117	125414	15	319	125748	0.00133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.750	625	574	1.09	0.0000307	8465
Missense in Polyphen		176	167.77	1.0491		2659
Synonymous	-1.26	245	221	1.11	0.0000121	2587
Loss of Function	0.468	51	54.7	0.932	0.00000250	789

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00401	0.00401
Ashkenazi Jewish	0.000135	0.0000992
East Asian	0.000925	0.000925
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00158	0.00138
Middle Eastern	0.000925	0.000925
South Asian	0.00221	0.00213
Other	0.00171	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of tight junction formation. Binds phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2). {ECO:0000269|PubMed:19706687}.

Recessive Scores

• pRec: 0.0910

Intolerance Scores

• loftool: 0.895
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.15

Haploinsufficiency Scores

• pHI: 0.0161
• hipred: N
• hipred_score: 0.146
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frmpd2

Gene ontology

• Biological process: bicellular tight junction assembly
• Cellular component: cytoplasm;cytoskeleton;bicellular tight junction;basolateral plasma membrane
• Molecular function: protein binding;1-phosphatidylinositol binding