FLRT1

fibronectin leucine rich transmembrane protein 1, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 11:64035931-64119173

Links

ENSG00000126500 ∙ NCBI:23769 ∙ OMIM:604806 ∙ HGNC:3760 ∙ Uniprot:Q9NZU1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spastic paraplegia, optic atropy, and neuropathy (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FLRT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FLRT1 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	42	19	62
missense			88	7	1	96
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	90	49	20

Variants in FLRT1

This is a list of pathogenic ClinVar variants found in the FLRT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64116299-C-A		not specified	Uncertain significance (Feb 28, 2023)
11-64116303-C-T		Peripheral neuropathy	Likely benign (Feb 11, 2020)
11-64116305-C-G		Peripheral neuropathy • not specified	Uncertain significance (Nov 06, 2023)
11-64116305-C-T		Peripheral neuropathy	Uncertain significance (Jul 19, 2022)
11-64116320-TCACGGCCACCGTTGTGATGAC-T		Peripheral neuropathy	Uncertain significance (Jun 19, 2018)
11-64116324-G-A		Peripheral neuropathy	Benign (Jul 03, 2019)
11-64116331-G-A		Peripheral neuropathy • FLRT1-related disorder	Conflicting classifications of pathogenicity (Aug 16, 2022)
11-64116353-T-A		Peripheral neuropathy	Uncertain significance (Feb 05, 2020)
11-64116361-C-A		Peripheral neuropathy	Likely benign (Jan 06, 2022)
11-64116375-C-T		Peripheral neuropathy • FLRT1-related disorder	Benign (Sep 19, 2022)
11-64116381-C-G		not specified	Uncertain significance (Oct 25, 2023)
11-64116384-C-T		Peripheral neuropathy	Benign (Nov 15, 2022)
11-64116390-C-T		Peripheral neuropathy	Likely benign (Feb 19, 2021)
11-64116422-C-G		not specified	Uncertain significance (Dec 27, 2023)
11-64116443-G-A		Peripheral neuropathy	Uncertain significance (Nov 22, 2022)
11-64116447-C-T		Peripheral neuropathy	Likely benign (Sep 28, 2018)
11-64116453-C-T		Peripheral neuropathy	Likely benign (Nov 16, 2020)
11-64116454-G-A		not specified	Uncertain significance (Jun 03, 2022)
11-64116478-G-C		Peripheral neuropathy • not specified	Uncertain significance (Feb 11, 2022)
11-64116495-C-T		Peripheral neuropathy	Likely benign (Apr 10, 2020)
11-64116496-G-A		Peripheral neuropathy	Uncertain significance (Sep 30, 2017)
11-64116513-T-C		Peripheral neuropathy	Benign (Jan 22, 2024)
11-64116518-C-T		Peripheral neuropathy • not specified	Uncertain significance (May 24, 2023)
11-64116552-C-T		Peripheral neuropathy	Likely benign (Oct 28, 2020)
11-64116555-C-T		Peripheral neuropathy	Benign (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FLRT1	protein_coding	protein_coding	ENST00000246841	1	15986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.357	0.641	125720	0	4	125724	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	372	466	0.798	0.0000324	4352
Missense in Polyphen		91	151.31	0.60141		1472
Synonymous	0.532	213	223	0.955	0.0000168	1492
Loss of Function	2.60	3	13.2	0.227	5.66e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000886	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000670	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in fibroblast growth factor-mediated signaling cascades that lead to the activation of MAP kinases. Promotes neurite outgrowth via FGFR1-mediated activation of downstream MAP kinases. Promotes an increase both in neurite number and in neurite length. May play a role in cell-cell adhesion and cell guidance via its interaction with ADGRL1/LPHN1 and ADGRL3. {ECO:0000250|UniProtKB:Q6RKD8}.
• Pathway: Signal Transduction;Signaling by FGFR;Signaling by Receptor Tyrosine Kinases;Downstream signaling of activated FGFR1;Signaling by FGFR1 (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.0504
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.78

Haploinsufficiency Scores

• pHI: 0.0624
• hipred: N
• hipred_score: 0.495
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.298

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Flrt1
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: flrt1b
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: viability

Gene ontology

• Biological process: cell adhesion;fibroblast growth factor receptor signaling pathway;dendrite development;positive regulation of synapse assembly;neuron projection extension
• Cellular component: extracellular space;endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;cell-cell junction;focal adhesion;cytoplasmic vesicle membrane;extracellular matrix;cytoplasmic vesicle;neuronal cell body membrane;neuron projection terminus;perinuclear region of cytoplasm
• Molecular function: fibroblast growth factor receptor binding;protein binding, bridging