FRMD3

FERM domain containing 3, the group of FERM domain containing

Basic information

Region (hg38): 9:83242989-83538546

Links

ENSG00000172159 ∙ NCBI:257019 ∙ OMIM:607619 ∙ HGNC:24125 ∙ Uniprot:A2A2Y4 ∙ 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 FRMD3 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRMD3 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						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in FRMD3

This is a list of pathogenic ClinVar variants found in the FRMD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-83247964-A-G		not specified	Uncertain significance (Jul 14, 2021)
9-83248040-A-G		not specified	Uncertain significance (May 15, 2023)
9-83248175-C-T		not specified	Uncertain significance (Sep 20, 2023)
9-83248238-C-T		not specified	Uncertain significance (May 18, 2022)
9-83248282-C-T		not specified	Uncertain significance (Oct 05, 2021)
9-83248349-G-A		not specified	Uncertain significance (Mar 01, 2023)
9-83248403-C-T		not specified	Uncertain significance (Mar 24, 2023)
9-83290624-C-T		not specified	Uncertain significance (May 24, 2023)
9-83290720-T-C		not specified	Uncertain significance (Dec 16, 2022)
9-83298781-G-A		not specified	Uncertain significance (Dec 15, 2023)
9-83298791-C-G		not specified	Uncertain significance (Aug 04, 2021)
9-83309551-T-C		not specified	Uncertain significance (Dec 09, 2023)
9-83309609-C-T		not specified	Uncertain significance (Feb 15, 2023)
9-83310498-C-T		not specified	Uncertain significance (Mar 23, 2023)
9-83311905-C-G		not specified	Uncertain significance (Jul 14, 2021)
9-83335540-A-C		not specified	Uncertain significance (Apr 25, 2022)
9-83335595-T-A		not specified	Uncertain significance (Dec 22, 2023)
9-83335596-G-A			Likely benign (Mar 01, 2024)
9-83335609-T-C		not specified	Uncertain significance (Dec 26, 2023)
9-83335625-A-C		not specified	Uncertain significance (Apr 28, 2023)
9-83343244-G-A		not specified	Uncertain significance (Oct 26, 2022)
9-83349712-T-C		not specified	Uncertain significance (Oct 02, 2023)
9-83389605-C-G		not specified	Uncertain significance (Aug 13, 2021)
9-83389643-G-T		not specified	Uncertain significance (Jul 26, 2022)
9-83538095-C-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRMD3	protein_coding	protein_coding	ENST00000304195	14	295557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.270	0.730	124765	0	31	124796	0.000124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.879	267	311	0.860	0.0000151	3941
Missense in Polyphen		75	98.651	0.76025		1284
Synonymous	-2.01	143	115	1.24	0.00000574	1102
Loss of Function	3.87	7	29.8	0.235	0.00000133	395

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00140	0.00139
East Asian	0.000112	0.000111
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000990	0.0000971
Middle Eastern	0.000112	0.000111
South Asian	0.0000327	0.0000327
Other	0.000332	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative tumor suppressor gene that may be implicated in the origin and progression of lung cancer. {ECO:0000269|PubMed:17260017}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.228
• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.05

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.554
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frmd3

Gene ontology

• Biological process: actomyosin structure organization
• Cellular component: cytoskeleton;integral component of membrane
• Molecular function: cytoskeletal protein binding