FRMD3

FERM domain containing 3, the group of FERM domain containing

Basic information

Region (hg38): 9:83242990-83538546

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.

• not_specified (63 variants)
• not_provided (1 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. These statistics are base on transcript: NM_000174938.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			63			63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	1	0

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