PDGFRL

protein-coding

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

Gene summary

This gene encodes a protein with significant sequence similarity to the ligand binding domain of platelet-derived growth factor receptor beta. Mutations in this gene, or deletion of a chromosomal segment containing this gene, are associated with sporadic hepatocellular carcinomas, colorectal cancers, and non-small cell lung cancers. This suggests this gene product may function as a tumor suppressor. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001372073.1

Inheritance

—

ClinVar variants

P:1U:90B:7

Top phenotype

Carcinoma of colon

gnomAD constraint

pLI —, LoF o/e 1.27

Max pathogenic AF

—

Genomic locus

chr8:17,576,433-17,644,071

External References & Databases

Ensembl (ENSG00000104213)

Transcript & Mutation Effects

hg38 • Region Span ~67.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDGFRL variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 7

Carcinoma of colonTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001372073.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	1 clinvar	5
missense	1 clinvar		85 clinvar	3 clinvar	1 clinvar	90
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	90	5	2	98

Highest pathogenic variant AF is 0.000004793122

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001372073.1	RefSeq	NP_001359002.1	6	MANE Select
ENST00000251630.11	Ensembl	ENSP00000251630.4	6	MANE Select
NM_006207.2	RefSeq	NP_006198.1	6	Standard
ENST00000541323.1	Ensembl	ENSP00000444211.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

G protein-coupled receptor signaling pathway
biological_process
platelet-derived growth factor receptor-beta signaling pathway

Molecular Function

platelet activating factor receptor activity
platelet-derived growth factor beta-receptor activity

Cellular Component

cellular_component
extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000541323
Coding exons: 6
Length: 67639
Individuals with no LoFs: 125577
Homozygous LoFs: 0
Heterozygous LoFs: 171
Defined: 125748
p: 0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.00	303	220	1.38	0.0000127	2428
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.0021	0.0021	notable
East Asian	0.0016	0.0016	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00076	0.00075	rare
South Asian	0.00033	0.00033	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.715

Gene Damage Prediction

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