Genetic Variant PTPRD:c.5534+7_5534+8insACAGTTCAGGAATGGTAAGTT (chr9-8331574-A-AAACTTACCATTCCTGAACTGT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_002839.4(PTPRD):c.5534+7_5534+8insACAGTTCAGGAATGGTAAGTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,607,146 control chromosomes in the GnomAD database, including 18,470 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 1929 hom., cov: 0)

Exomes 𝑓: 0.13 ( 16541 hom. )

Consequence

PTPRD
NM_002839.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.111

Publications

3 publications found

Variant links:

Genes affected

PTPRD (HGNC:9668): (protein tyrosine phosphatase receptor type D) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an extracellular region, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this protein is composed of three Ig-like and eight fibronectin type III-like domains. Studies of the similar genes in chicken and fly suggest the role of this PTP is in promoting neurite growth, and regulating neurons axon guidance. Multiple alternatively spliced transcript variants of this gene have been reported. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Jan 2010]

PTPRD links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4 link	c.5534+7_5534+8insACAGTTCAGGAATGGTAAGTT		splice_region_variant, intron_variant	Intron 44 of 45	ENST00000381196.9	NP_002830.1	P23468-1Q2HXI4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9 link	c.5534+7_5534+8insACAGTTCAGGAATGGTAAGTT		splice_region_variant, intron_variant	Intron 44 of 45	5	NM_002839.4	ENSP00000370593.3		P23468-1

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21227

AN:

151868

Hom.:

1925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.124

GnomAD4 exome

AF:

0.134

AC:

194426

AN:

1455162

Hom.:

16541

Cov.:

AF XY:

0.134

AC XY:

96820

AN XY:

724272

show subpopulations

African (AFR)

AF:

0.0959

AC:

3202

AN:

33388

American (AMR)

AF:

0.377

AC:

16798

AN:

44556

Ashkenazi Jewish (ASJ)

AF:

0.0953

AC:

2486

AN:

26096

East Asian (EAS)

AF:

0.349

AC:

13793

AN:

39566

South Asian (SAS)

AF:

0.193

AC:

16577

AN:

85956

European-Finnish (FIN)

AF:

0.145

AC:

7696

AN:

53206

Middle Eastern (MID)

AF:

0.0703

AC:

404

AN:

5748

European-Non Finnish (NFE)

AF:

0.113

AC:

125246

AN:

1106518

Other (OTH)

AF:

0.137

AC:

8224

AN:

60128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

6171

12343

18514

24686

30857

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.140

AC:

21239

AN:

151984

Hom.:

1929

Cov.:

AF XY:

0.147

AC XY:

10907

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.105

AC:

4347

AN:

41424

American (AMR)

AF:

0.269

AC:

4110

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

347

AN:

3470

East Asian (EAS)

AF:

0.346

AC:

1785

AN:

5156

South Asian (SAS)

AF:

0.199

AC:

958

AN:

4816

European-Finnish (FIN)

AF:

0.151

AC:

1603

AN:

10592

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7783

AN:

67970

Other (OTH)

AF:

0.126

AC:

265

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

867

1733

2600

3466

4333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0876

Hom.:

255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.11

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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9-8331574-A-AAACTTACCATTCCTGAACTGT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over