PDGFRL

platelet derived growth factor receptor like, the group of I-set domain containing

Basic information

Region (hg38): 8:17576432-17644071

Links

ENSG00000104213 ∙ NCBI:5157 ∙ OMIM:604584 ∙ HGNC:8805 ∙ Uniprot:Q15198 ∙ 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 PDGFRL gene.

• Inborn genetic diseases (18 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDGFRL 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	2
missense			18	2	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	2

Variants in PDGFRL

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

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

Position	Type	Phenotype	Significance	ClinVar
8-17577264-G-T			Likely benign (Feb 09, 2018)
8-17577291-C-G		not specified	Uncertain significance (Sep 01, 2021)
8-17589479-C-T		Carcinoma of colon	Pathogenic (Mar 02, 1995)
8-17589563-A-G		not specified	Uncertain significance (Mar 27, 2023)
8-17589618-T-C			Benign (Feb 09, 2018)
8-17589653-G-A		not specified	Uncertain significance (Aug 04, 2023)
8-17589661-C-A			Benign (Feb 09, 2018)
8-17589698-T-C		not specified	Uncertain significance (Dec 20, 2023)
8-17589724-C-G		not specified	Uncertain significance (May 11, 2022)
8-17589758-C-T		not specified	Uncertain significance (Aug 16, 2022)
8-17589759-G-A		not specified	Uncertain significance (Nov 09, 2023)
8-17621070-T-C		not specified	Uncertain significance (Oct 12, 2021)
8-17621073-G-A		not specified	Uncertain significance (Dec 13, 2022)
8-17621101-C-T		not specified	Uncertain significance (Dec 13, 2021)
8-17621105-A-G			Likely benign (Feb 01, 2023)
8-17621188-A-G		not specified	Uncertain significance (Dec 26, 2023)
8-17628513-C-T		not specified	Uncertain significance (Sep 26, 2023)
8-17628765-C-G		not specified	Uncertain significance (Apr 25, 2022)
8-17634074-T-A		not specified	Uncertain significance (Mar 29, 2023)
8-17634081-T-G		not specified	Uncertain significance (Jun 22, 2023)
8-17634086-C-G		not specified	Uncertain significance (Nov 09, 2023)
8-17634095-C-A		not specified	Uncertain significance (Jun 06, 2023)
8-17634095-C-T		not specified	Uncertain significance (Jul 26, 2022)
8-17634097-A-G		not specified	Uncertain significance (Jul 25, 2023)
8-17634107-C-T		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDGFRL	protein_coding	protein_coding	ENST00000541323	6	67639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-14	0.00314	125577	0	171	125748	0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.00	303	220	1.38	0.0000127	2428
Missense in Polyphen		88	70.237	1.2529		799
Synonymous	-2.62	125	92.9	1.35	0.00000619	757
Loss of Function	-0.961	19	15.0	1.27	7.01e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000604	0.000603
Ashkenazi Jewish	0.00211	0.00209
East Asian	0.00163	0.00163
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000758	0.000747
Middle Eastern	0.00163	0.00163
South Asian	0.000329	0.000327
Other	0.00133	0.00130

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A polymorphism in PDGFRL has been reported to be associated with susceptibility to Behcet disease (PubMed:22926996). Behcet disease is a complex multiple-system disorder characterized by recurrent oral ulcerations, recurrent genital ulcerations, typical skin lesions, and uveitis. Behcet disease also involves joints, blood vessels, musculoskeletal, neurological systems, and the gastrointestinal tract. {ECO:0000269|PubMed:22926996}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.892
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.24

Haploinsufficiency Scores

• pHI: 0.283
• hipred: N
• hipred_score: 0.251
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.715

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdgfrl

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;biological_process;platelet-derived growth factor receptor-beta signaling pathway
• Cellular component: cellular_component;extracellular region
• Molecular function: platelet activating factor receptor activity;platelet-derived growth factor beta-receptor activity