FMNL3

formin like 3, the group of Formins|Armadillo like helical domain containing

Basic information

Region (hg38): 12:49636499-49708165

Links

ENSG00000161791 ∙ NCBI:91010 ∙ OMIM:616288 ∙ HGNC:23698 ∙ Uniprot:Q8IVF7 ∙ 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 FMNL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FMNL3 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			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			28	1		29
Total	0	0	80	2	0

Variants in FMNL3

This is a list of pathogenic ClinVar variants found in the FMNL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-49636718-A-G		not specified	Uncertain significance (May 08, 2024)
12-49636719-T-C		not specified	Uncertain significance (Apr 01, 2024)
12-49636791-G-A		not specified	Uncertain significance (Sep 20, 2023)
12-49636808-C-T		not specified	Uncertain significance (Sep 30, 2021)
12-49637554-G-A		not specified	Uncertain significance (Jan 10, 2022)
12-49637555-T-C		not specified	Uncertain significance (Oct 12, 2021)
12-49637760-T-A		not specified	Uncertain significance (Dec 11, 2023)
12-49637810-A-C		not specified	Uncertain significance (Dec 26, 2023)
12-49641923-G-C		not specified	Uncertain significance (Aug 12, 2021)
12-49641939-C-T		not specified	Uncertain significance (Feb 13, 2024)
12-49641956-C-T		not specified	Uncertain significance (Jan 08, 2024)
12-49641986-G-A		not specified	Uncertain significance (Jun 17, 2024)
12-49642247-G-T		not specified	Uncertain significance (Dec 11, 2023)
12-49642256-C-T		not specified	Uncertain significance (Jul 20, 2021)
12-49642269-G-A		not specified	Uncertain significance (May 09, 2023)
12-49642273-G-C		not specified	Uncertain significance (Sep 27, 2021)
12-49642274-A-G		not specified	Uncertain significance (May 24, 2024)
12-49642296-G-A		not specified	Uncertain significance (Jan 17, 2024)
12-49642299-G-A		not specified	Uncertain significance (Aug 26, 2022)
12-49642336-T-A			Likely benign (Mar 01, 2024)
12-49642584-G-A		not specified	Uncertain significance (Oct 30, 2023)
12-49642632-C-T		not specified	Uncertain significance (Nov 27, 2023)
12-49642997-A-G		not specified	Uncertain significance (Nov 02, 2023)
12-49643244-G-C		not specified	Uncertain significance (Mar 31, 2024)
12-49643272-C-G		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FMNL3	protein_coding	protein_coding	ENST00000335154	26	70225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.465	0.535	125315	0	35	125350	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	449	601	0.747	0.0000372	6713
Missense in Polyphen		253	361.01	0.70082		4052
Synonymous	-0.635	245	233	1.05	0.0000129	2018
Loss of Function	5.30	12	54.1	0.222	0.00000289	625

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000254	0.000243
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000222	0.000218
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.000222	0.000218
South Asian	0.000197	0.000196
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape and migration. Required for developmental angiogenesis (By similarity). In this process, required for microtubule reorganization and for efficient endothelial cell elongation. In quiescent endothelial cells, triggers rearrangement of the actin cytoskeleton, but does not alter microtubule alignement. {ECO:0000250|UniProtKB:Q6NXC0, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:22275430}.
• Pathway: Signal Transduction;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.214
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8.1

Haploinsufficiency Scores

• pHI: 0.125
• hipred: Y
• hipred_score: 0.563
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fmnl3
• Phenotype: 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); hearing/vestibular/ear phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: fmnl3
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: angiogenesis;cytoskeleton organization;regulation of cell shape;cell migration;actin cytoskeleton organization
• Cellular component: cytoplasm;Golgi apparatus;cytosol;plasma membrane;intracellular membrane-bounded organelle
• Molecular function: actin binding;Rho GTPase binding;GTPase activating protein binding