FMN1

formin 1, the group of Formins

Basic information

Region (hg38): 15:32765543-33194714

Previous symbols: [ "LD", "FMN" ]

Links

ENSG00000248905 ∙ NCBI:342184 ∙ OMIM:136535 ∙ HGNC:3768 ∙ Uniprot:Q68DA7 ∙ 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 FMN1 gene.

• not provided (275 variants)
• Inborn genetic diseases (69 variants)
• not specified (26 variants)
• FMN1-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FMN1 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			11	28	22	61
missense			115	20	36	171
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel			3	1	2	6
splice donor/acceptor (+/-2bp)						0
splice region				5		5
non coding			1	10	74	85
Total	0	0	132	59	134

Variants in FMN1

This is a list of pathogenic ClinVar variants found in the FMN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-32774126-G-A			Benign (May 12, 2021)
15-32774277-C-T			Benign (May 12, 2021)
15-32774309-C-T		not specified • FMN1-related disorder	Likely benign (Mar 29, 2019)
15-32774324-C-T		not specified	Uncertain significance (Oct 03, 2022)
15-32774325-A-C			Likely benign (Dec 07, 2022)
15-32774341-C-T		not specified	Uncertain significance (Aug 28, 2023)
15-32774363-G-GA			Likely benign (Jun 12, 2023)
15-32774368-A-G			Likely benign (Oct 31, 2022)
15-32774381-T-A			Benign (May 12, 2021)
15-32774521-CCCTA-C			Benign (May 12, 2021)
15-32776687-CT-C			Benign (May 11, 2021)
15-32776688-T-TTC			Benign (May 13, 2021)
15-32776826-A-G			Benign (Oct 05, 2023)
15-32776918-A-G			Likely benign (Dec 06, 2022)
15-32777103-G-A			Benign (May 12, 2021)
15-32798683-T-G			Benign (May 12, 2021)
15-32798813-G-C		not specified	Uncertain significance (Mar 25, 2022)
15-32798832-G-C		not specified	Uncertain significance (Jan 10, 2022)
15-32798875-C-T			Uncertain significance (Jul 25, 2022)
15-32798878-A-G			Benign (Jan 29, 2024)
15-32798883-C-A			Uncertain significance (Dec 01, 2021)
15-32798883-C-T		not specified • FMN1-related disorder	Likely benign (Jul 13, 2022)
15-32798901-CCTT-C		not specified	Benign (Jan 29, 2024)
15-32798934-A-G			Uncertain significance (Sep 19, 2022)
15-32798936-C-T		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FMN1	protein_coding	protein_coding	ENST00000334528	17	429151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.59e-18	0.635	124478	0	177	124655	0.000710

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.53	721	614	1.17	0.0000323	7769
Missense in Polyphen		111	138.21	0.80315		1867
Synonymous	-3.43	306	239	1.28	0.0000135	2316
Loss of Function	1.93	35	49.7	0.704	0.00000253	664

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00210	0.00209
Ashkenazi Jewish	0.000309	0.000298
East Asian	0.000955	0.000946
Finnish	0.000613	0.000603
European (Non-Finnish)	0.000609	0.000584
Middle Eastern	0.000955	0.000946
South Asian	0.000893	0.000883
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the formation of adherens junction and the polymerization of linear actin cables. {ECO:0000250}.
• Pathway: E-cadherin signaling in keratinocytes (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.991
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.64

Haploinsufficiency Scores

• pHI: 0.272
• hipred: N
• hipred_score: 0.222
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.670

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fmn1
• Phenotype: skeleton phenotype; renal/urinary system phenotype; limbs/digits/tail phenotype; reproductive system 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); normal phenotype; pigmentation phenotype; cellular 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)

Gene ontology

• Biological process: gene expression;forelimb morphogenesis;hindlimb morphogenesis;actin nucleation;skeletal system morphogenesis;positive regulation of actin nucleation;positive regulation of focal adhesion assembly;ureteric bud invasion
• Cellular component: nucleus;cytoplasm;actin filament;plasma membrane;adherens junction
• Molecular function: actin binding;microtubule binding;SH3 domain binding