NM_002609.4:c.2362C>G

Variant names:

• chr5-150121305-G-C
• rs1320275282
• NM_002609.4:c.2362C>G
• PDGFRB p.Arg788Gly

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+2 Uncertain · Warm

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

The NM_002609.4(PDGFRB):c.2362C>G (p.Arg788Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The gene PDGFRB is a known oncogene (CancerMine: 11 oncogene, 19 driver citations). The gene PDGFRB is a cancer driver gene (CancerMine: 11 oncogene, 19 driver citations). The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.R788*: Uncertain_significance (ClinVar VariationId 520866, 2 stars)

• Frequency: Genomes: not found (cov: 32)
• Consequence: PDGFRB NM_002609.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73
• Publications: 0 publications found

Genes affected

PDGFRB (HGNC:8804): (platelet derived growth factor receptor beta) The protein encoded by this gene is a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor family. These growth factors are mitogens for cells of mesenchymal origin. The identity of the growth factor bound to a receptor monomer determines whether the functional receptor is a homodimer (PDGFB or PDGFD) or a heterodimer (PDGFA and PDGFB). This gene is essential for normal development of the cardiovascular system and aids in rearrangement of the actin cytoskeleton. This gene is flanked on chromosome 5 by the genes for granulocyte-macrophage colony-stimulating factor and macrophage-colony stimulating factor receptor; all three genes may be implicated in the 5-q syndrome. A translocation between chromosomes 5 and 12, that fuses this gene to that of the ETV6 gene, results in chronic myeloproliferative disorder with eosinophilia. [provided by RefSeq, Aug 2017]

PDGFRB Gene-Disease associations (from GenCC):

• acroosteolysis-keloid-like lesions-premature aging syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, G2P, Orphanet, Labcorp Genetics (formerly Invitae)
• myofibromatosis, infantile, 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia
• basal ganglia calcification, idiopathic, 4

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Genomics England PanelApp, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• bilateral striopallidodentate calcinosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• infantile myofibromatosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary progressive mucinous histiocytosis

  Inheritance: AD Classification: LIMITED Submitted by: G2P
• ocular pterygium-digital keloid dysplasia syndrome

  Inheritance: AD Classification: LIMITED Submitted by: PanelApp Australia

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_002609.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	PDGFRB NM_002609.4	MANE Select	c.2362C>G p.Arg788Gly	missense	Exon 17 of 23	Prot: NP_002600.1 UniProt:
	PDGFRB NM_001355016.2		c.2170C>G p.Arg724Gly	missense	Exon 16 of 22	Prot: NP_001341945.1
	PDGFRB NM_001355017.2		c.1879C>G p.Arg627Gly	missense	Exon 17 of 23	Prot: NP_001341946.1

PDGFRB NM_002609.4

MANE Select

HGVSc / HGVSpc.2362C>Gp.Arg788Gly

Exon rankExon 17 of 23

missense

Prot: NP_002600.1UniProt: P09619-1

PDGFRB NM_001355016.2

HGVSc / HGVSpc.2170C>Gp.Arg724Gly

Exon rankExon 16 of 22

missense

Prot: NP_001341945.1

PDGFRB NM_001355017.2

HGVSc / HGVSpc.1879C>Gp.Arg627Gly

Exon rankExon 17 of 23

missense

Prot: NP_001341946.1

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	PDGFRB ENST00000261799.9	TSL:1MANE Select	c.2362C>G p.Arg788Gly	missense	Exon 17 of 23	Prot: ENSP00000261799.4 UniProt:
	PDGFRB ENST00000520579.5	TSL:1	n.*1676C>G	3_prime_UTR	Exon 17 of 23	Prot: ENSP00000430026.1 UniProt:
	PDGFRB ENST00000520579.5	TSL:1	n.*1676C>G	non_coding_transcript_exon	Exon 17 of 23	Prot: ENSP00000430026.1 UniProt:

PDGFRB ENST00000261799.9

TSL:1MANE Select

HGVSc / HGVSpc.2362C>Gp.Arg788Gly

Exon rankExon 17 of 23

missense

Prot: ENSP00000261799.4UniProt: P09619-1

PDGFRB ENST00000520579.5

TSL:1

HGVSc / HGVSpn.*1676C>G

Exon rankExon 17 of 23

3_prime_UTR

Prot: ENSP00000430026.1UniProt: E5RH16

PDGFRB ENST00000520579.5

TSL:1

HGVSc / HGVSpn.*1676C>G

Exon rankExon 17 of 23

non_coding_transcript_exon

Prot: ENSP00000430026.1UniProt: E5RH16

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:27
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	20
AlphaMissense	Benign	0.10
BayesDel_addAF	Uncertain	0.063	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.57	D
Eigen	Benign	-0.051
Eigen_PC	Benign	-0.19
FATHMM_MKL	Benign	0.51	D
FuncVEP CTI	Benign	0.13
GPN-Star LLR	N/A	-6.5
GPN-Star score	N/A	6.5
LIST_S2	Uncertain	0.86	D
M_CAP	Uncertain	0.14	D
MetaRNN	Uncertain	0.67	D
MetaSVM	Uncertain	-0.047	T
Mutation Taster	N/A	86/14	polymorphism
MutationAssessor	Benign	1.2	L
PhyloP100	Benign	2.7
popEVE	Benign	-3.2
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-2.2	N
REVEL	Uncertain	0.30
Sift	Benign	0.071	T
Sift4G	Benign	0.23	T
Varity_R	N/A	0.14
VESM-3B	Benign	-5.7

Showing 28 of 28 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs1320275282;

hg19: chr5-149500868;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar