FRMD4B

FERM domain containing 4B, the group of FERM domain containing

Basic information

Region (hg38): 3:69168781-69542583

Links

ENSG00000114541 ∙ NCBI:23150 ∙ OMIM:617467 ∙ HGNC:24886 ∙ Uniprot:Q9Y2L6 ∙ 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 FRMD4B gene.

• Inborn genetic diseases (42 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRMD4B 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			40	3		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	4	0

Variants in FRMD4B

This is a list of pathogenic ClinVar variants found in the FRMD4B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-69171928-T-A		not specified	Uncertain significance (Oct 03, 2022)
3-69171953-C-G		not specified	Uncertain significance (Sep 14, 2023)
3-69171966-G-C		not specified	Uncertain significance (Nov 22, 2023)
3-69176608-C-T		not specified	Uncertain significance (Dec 07, 2021)
3-69180919-C-T		not specified	Uncertain significance (Dec 20, 2023)
3-69180976-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-69181003-G-A		not specified	Likely benign (Aug 02, 2022)
3-69181018-T-C		not specified	Uncertain significance (Apr 22, 2022)
3-69181073-C-A			Likely benign (Jun 20, 2018)
3-69181147-T-A		not specified	Uncertain significance (Feb 27, 2023)
3-69181159-C-T		not specified	Uncertain significance (Dec 13, 2023)
3-69181175-C-T		not specified	Uncertain significance (Sep 27, 2022)
3-69181204-C-T		not specified	Uncertain significance (Mar 02, 2023)
3-69181232-G-A		not specified	Uncertain significance (Dec 01, 2022)
3-69181280-C-T		not specified	Uncertain significance (Jul 20, 2022)
3-69181308-C-G		not specified	Uncertain significance (Jun 09, 2022)
3-69181360-T-C		not specified	Uncertain significance (Jun 21, 2023)
3-69181403-C-G		not specified	Uncertain significance (Apr 24, 2023)
3-69181454-A-T		not specified	Uncertain significance (Jun 06, 2023)
3-69181462-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-69181471-G-C		not specified	Uncertain significance (Jun 22, 2021)
3-69181486-G-T		not specified	Uncertain significance (Jan 29, 2024)
3-69181696-G-C		not specified	Uncertain significance (May 27, 2022)
3-69182640-G-A		not specified	Uncertain significance (Jul 09, 2021)
3-69182649-A-G		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRMD4B	protein_coding	protein_coding	ENST00000398540	23	372594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.454	0.546	124618	0	19	124637	0.0000762

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0405	547	544	1.00	0.0000292	6671
Missense in Polyphen		224	229.02	0.97808		2733
Synonymous	-0.402	220	213	1.04	0.0000121	1924
Loss of Function	5.71	14	62.8	0.223	0.00000360	729

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000569	0.0000556
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000820	0.0000796
Middle Eastern	0.0000569	0.0000556
South Asian	0.000100	0.0000980
Other	0.000187	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Member of GRP1 signaling complexes that are acutely recruited to plasma membrane ruffles in response to insulin receptor signaling. May function as a scaffolding protein that regulates epithelial cell polarity by connecting ARF6 activation with the PAR3 complex. Plays a redundant role with FRMD4A in epithelial polarization. {ECO:0000250|UniProtKB:Q920B0}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.114
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.52

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.475
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.152

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frmd4b
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: establishment of epithelial cell polarity
• Cellular component: ruffle;extracellular space;cytoplasm;cytoskeleton;adherens junction;bicellular tight junction