FGFRL1

fibroblast growth factor receptor like 1, the group of I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 4:1009935-1026898

Links

ENSG00000127418 ∙ NCBI:53834 ∙ OMIM:605830 ∙ HGNC:3693 ∙ Uniprot:Q8N441 ∙ 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 FGFRL1 gene.

• not provided (211 variants)
• Inborn genetic diseases (41 variants)
• Congenital diaphragmatic hernia (2 variants)
• 4p partial monosomy syndrome (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGFRL1 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				67	13	80
missense			111	9	5	125
nonsense						0
start loss						0
frameshift			2	2		4
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region				4		4
non coding				17	3	20
Total	0	0	115	95	21

Variants in FGFRL1

This is a list of pathogenic ClinVar variants found in the FGFRL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-1012498-C-T		not specified	Uncertain significance (Oct 13, 2023)
4-1012507-C-T			Likely benign (Jan 31, 2018)
4-1012519-C-T		not specified	Uncertain significance (May 18, 2023)
4-1012525-C-T			Likely benign (Feb 08, 2022)
4-1012530-G-C			Likely benign (Aug 04, 2023)
4-1012545-G-A		FGFRL1-related disorder	Benign (Jan 30, 2024)
4-1012548-GGCC-G			Uncertain significance (Nov 27, 2023)
4-1012551-C-T			Likely benign (May 12, 2023)
4-1012559-C-T			Uncertain significance (Sep 19, 2022)
4-1012560-C-T			Likely benign (May 30, 2022)
4-1012561-C-G		not specified	Uncertain significance (Aug 24, 2023)
4-1012577-G-T			Likely benign (Jan 01, 2024)
4-1012584-C-T			Likely benign (Jul 06, 2022)
4-1022194-C-T			Likely benign (Jan 04, 2018)
4-1022196-C-T			Likely benign (Apr 21, 2022)
4-1022203-G-T			Uncertain significance (May 23, 2023)
4-1022211-A-G			Uncertain significance (Nov 10, 2021)
4-1022218-C-T		FGFRL1-related disorder	Benign (Jan 22, 2024)
4-1022219-G-A			Likely benign (Apr 03, 2023)
4-1022236-G-A			Likely benign (Apr 25, 2023)
4-1022237-G-A			Likely benign (Jan 08, 2024)
4-1022240-G-C			Uncertain significance (Nov 01, 2021)
4-1022247-C-T		Flexion contracture	Uncertain significance (Dec 13, 2022)
4-1022265-C-T			Uncertain significance (Dec 13, 2023)
4-1022283-G-A			Uncertain significance (Feb 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FGFRL1	protein_coding	protein_coding	ENST00000398484	6	16962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0119	0.981	125198	0	14	125212	0.0000559

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.248	341	354	0.963	0.0000260	3151
Missense in Polyphen		119	150.98	0.78816		1305
Synonymous	-2.30	210	172	1.22	0.0000140	1104
Loss of Function	2.35	6	16.2	0.370	8.48e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000185
Ashkenazi Jewish	0.000117	0.0000997
East Asian	0.000115	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000365	0.0000354
Middle Eastern	0.000115	0.000109
South Asian	0.0000334	0.0000327
Other	0.000169	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a negative effect on cell proliferation. {ECO:0000250}.
• Pathway: VEGF Signaling Pathway;Signal Transduction;Signaling by FGFR;Signaling by Receptor Tyrosine Kinases;FGFRL1 modulation of FGFR1 signaling;Signaling by FGFR1 (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.101
• rvis_EVS: -0.77
• rvis_percentile_EVS: 13.1

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.748
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fgfrl1
• Phenotype: 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); hematopoietic system phenotype; normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; skeleton phenotype; renal/urinary system phenotype; muscle 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); growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: fgfrl1b
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: skeletal system development;heart valve morphogenesis;negative regulation of cell population proliferation;fibroblast growth factor receptor signaling pathway;substrate adhesion-dependent cell spreading;protein homooligomerization;protein heterooligomerization;ventricular septum morphogenesis;diaphragm development;cell-cell adhesion via plasma-membrane adhesion molecules
• Cellular component: Golgi apparatus;plasma membrane;integral component of membrane;transport vesicle;cell-cell contact zone
• Molecular function: fibroblast growth factor-activated receptor activity;heparin binding;fibroblast growth factor binding