FMNL2

formin like 2, the group of Formins|Armadillo like helical domain containing

Basic information

Region (hg38): 2:152335173-152649826

Previous symbols: [ "FHOD2" ]

Links

ENSG00000157827 ∙ NCBI:114793 ∙ OMIM:616285 ∙ HGNC:18267 ∙ Uniprot:Q96PY5 ∙ 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 FMNL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FMNL2 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			31	2	1	34
nonsense						0
start loss						0
frameshift			1			1
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding				1		1
Total	0	0	32	4	2

Variants in FMNL2

This is a list of pathogenic ClinVar variants found in the FMNL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-152335646-A-G		not specified	Uncertain significance (May 12, 2024)
2-152521945-T-C			Benign (Mar 22, 2022)
2-152549034-G-C		not specified	Uncertain significance (Jun 17, 2024)
2-152549066-C-G			Likely benign (Aug 08, 2018)
2-152558730-T-TGTTTTTTTTTC			Likely benign (Jan 12, 2024)
2-152558787-T-C		Crohn disease	Likely pathogenic (Feb 20, 2021)
2-152558819-G-T		not specified	Uncertain significance (Apr 08, 2022)
2-152560945-G-T		not specified	Uncertain significance (Jun 24, 2022)
2-152561011-G-A		not specified	Uncertain significance (Jan 16, 2024)
2-152561043-C-G			Likely benign (Jul 06, 2018)
2-152578956-G-T		not specified	Uncertain significance (Nov 30, 2022)
2-152580961-A-C		not specified	Uncertain significance (Feb 28, 2023)
2-152580964-C-G		FMNL2-related disorder	Uncertain significance (Jul 24, 2023)
2-152580990-G-A		not specified	Uncertain significance (Jun 18, 2021)
2-152607357-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-152607358-G-A		FMNL2-related disorder • not specified	Uncertain significance (Jun 25, 2023)
2-152611598-A-G			Benign (Jul 19, 2018)
2-152617138-T-G		not specified	Uncertain significance (Jun 02, 2023)
2-152618997-G-A		not specified	Uncertain significance (Mar 15, 2024)
2-152619005-G-A		not specified	Uncertain significance (Nov 12, 2021)
2-152619033-C-T		not specified	Uncertain significance (Feb 21, 2024)
2-152619045-G-A		not specified	Uncertain significance (Sep 15, 2021)
2-152619149-C-T			Likely benign (Jul 02, 2018)
2-152619514-A-G		not specified	Uncertain significance (Dec 21, 2022)
2-152619552-G-GCCA		FMNL2-related disorder	Benign (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FMNL2	protein_coding	protein_coding	ENST00000288670	26	314598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00680	124731	0	13	124744	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.86	375	566	0.662	0.0000292	7135
Missense in Polyphen		38	84.406	0.45021		1112
Synonymous	1.71	179	210	0.850	0.0000110	2032
Loss of Function	5.72	9	54.6	0.165	0.00000277	719

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000943	0.0000938
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000566	0.0000556
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.0000457	0.0000442
Middle Eastern	0.0000566	0.0000556
South Asian	0.0000660	0.0000654
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the cortical actin filament dynamics. {ECO:0000269|PubMed:21834987}.
• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;EMT transition in Colorectal Cancer;Signal Transduction;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases (Consensus)

Intolerance Scores

• loftool: 0.156
• rvis_EVS: 0.14
• rvis_percentile_EVS: 63.62

Haploinsufficiency Scores

• pHI: 0.374
• hipred: Y
• hipred_score: 0.682
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.874

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fmnl2

Gene ontology

• Biological process: cytoskeleton organization;regulation of cell morphogenesis;cortical actin cytoskeleton organization
• Cellular component: cytosol
• Molecular function: actin binding;Rho GTPase binding;cadherin binding