FGFRL1

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

Basic information

Region (hg38): 4:1009936-1026898

Links

ENSG00000127418 ∙ NCBI:53834 ∙ OMIM:605830 ∙ HGNC:3693 ∙ Uniprot:Q8N441 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 19.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001004356.3	NP_001004356.1	6	yes	-
ENST00000510644.6	ENSP00000425025.1	6	yes	-
NM_021923.3	NP_068742.2	6	-	-
NM_001004358.1	NP_001004358.1	6	-	-

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 (288 variants)
• not_specified (122 variants)
• FGFRL1-related_disorder (20 variants)
• 4p_partial_monosomy_syndrome (2 variants)
• Congenital_diaphragmatic_hernia (2 variants)
• Microcephaly (1 variants)
• Flexion_contracture (1 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. These statistics are base on transcript: NM_001004356.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				97	10	107
missense			197	12	2	211
nonsense			1			1
start loss						0
frameshift			6	2		8
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	206	111	12

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
		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

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

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