FLRT2

fibronectin leucine rich transmembrane protein 2, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 14:85530144-85654428

Links

ENSG00000185070 ∙ NCBI:23768 ∙ OMIM:604807 ∙ HGNC:3761 ∙ Uniprot:O43155 ∙ 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 FLRT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FLRT2 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	1

Variants in FLRT2

This is a list of pathogenic ClinVar variants found in the FLRT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-85621596-T-G		not specified	Uncertain significance (Apr 22, 2022)
14-85621707-G-A		not specified	Uncertain significance (Dec 06, 2021)
14-85621804-G-T		not specified	Uncertain significance (Jul 13, 2021)
14-85621882-C-T		not specified	Uncertain significance (Dec 14, 2023)
14-85621911-T-G		not specified	Uncertain significance (Aug 30, 2022)
14-85621998-A-C		not specified	Uncertain significance (Jun 13, 2024)
14-85622040-G-T		not specified	Uncertain significance (Jun 29, 2022)
14-85622110-C-T		not specified	Uncertain significance (Mar 01, 2023)
14-85622173-G-C		not specified	Uncertain significance (Jun 29, 2022)
14-85622188-C-T		not specified	Uncertain significance (May 23, 2023)
14-85622223-A-T		not specified	Uncertain significance (Apr 24, 2023)
14-85622242-C-T		not specified	Uncertain significance (Feb 28, 2024)
14-85622316-C-T		not specified	Uncertain significance (Sep 21, 2023)
14-85622323-C-T		not specified	Uncertain significance (Oct 26, 2021)
14-85622340-C-T		not specified	Uncertain significance (Dec 21, 2022)
14-85622353-G-A		not specified	Uncertain significance (Oct 20, 2023)
14-85622436-C-T		not specified	Uncertain significance (Feb 06, 2023)
14-85622504-A-G			Benign (Jun 29, 2018)
14-85622626-C-T		not specified	Uncertain significance (Aug 08, 2022)
14-85622688-A-G			Likely benign (Jun 29, 2018)
14-85622712-C-G		not specified	Uncertain significance (Jan 10, 2022)
14-85622713-C-T		not specified	Uncertain significance (Sep 01, 2021)
14-85622734-C-T		not specified	Uncertain significance (Jun 06, 2023)
14-85622859-G-A		not specified	Uncertain significance (May 12, 2024)
14-85622899-T-C		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FLRT2	protein_coding	protein_coding	ENST00000330753	1	98547

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.817	0.183	125725	0	4	125729	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	314	384	0.817	0.0000237	4309
Missense in Polyphen		57	120.5	0.47301		1401
Synonymous	-1.70	189	161	1.17	0.0000103	1361
Loss of Function	3.37	3	18.8	0.160	0.00000112	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in cell-cell adhesion, cell migration and axon guidance. Mediates cell-cell adhesion via its interactions with ADGRL3 and probably also other latrophilins that are expressed at the surface of adjacent cells. May play a role in the migration of cortical neurons during brain development via its interaction with UNC5D. Mediates axon growth cone collapse and plays a repulsive role in neuron guidance via its interaction with UNC5D, and possibly also other UNC-5 family members. Plays a role in fibroblast growth factor-mediated signaling cascades. Required for normal organization of the cardiac basement membrane during embryogenesis, and for normal embryonic epicardium and heart morphogenesis. {ECO:0000250|UniProtKB:Q8BLU0}.
• Pathway: Signal Transduction;Signaling by FGFR;Signaling by Receptor Tyrosine Kinases;Downstream signaling of activated FGFR1;Signaling by FGFR1 (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.696
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.537

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Flrt2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: heart morphogenesis;axon guidance;biological_process;fibroblast growth factor receptor signaling pathway;negative chemotaxis;positive regulation of synapse assembly;cell adhesion involved in heart morphogenesis;basement membrane organization;regulation of neuron migration
• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;cell-cell junction;focal adhesion;extracellular matrix;organelle membrane;neuron projection;synapse;extracellular exosome
• Molecular function: fibroblast growth factor receptor binding;protein binding, bridging;chemorepellent activity