9-94085303-G-T

Variant names:

• chr9-94085303-G-T
• NM_001253829.2:c.297G>T
• PTPDC1 p.Arg99Arg

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001253829.2(PTPDC1):​c.297G>T​(p.Arg99Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: PTPDC1 NM_001253829.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 0 publications found

Genes affected

PTPDC1 (HGNC:30184): (protein tyrosine phosphatase domain containing 1) The protein encoded by this gene contains a characteristic motif of protein tyrosine phosphatases (PTPs). PTPs regulate activities of phosphoproteins through dephosphorylation. They are signaling molecules involved in the regulation of a wide variety of biological processes. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP7: Synonymous conserved (PhyloP=0.081 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001253829.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPDC1	NM_001253829.2	MANE Select	c.297G>T	p.Arg99Arg	synonymous	Exon 2 of 9	NP_001240758.1	A0A087WTF0
	PTPDC1	NM_152422.4		c.291G>T	p.Arg97Arg	synonymous	Exon 2 of 9	NP_689635.3	A2A3K4-2
	PTPDC1	NM_177995.3		c.135G>T	p.Arg45Arg	synonymous	Exon 3 of 10	NP_818931.1	A2A3K4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPDC1	ENST00000620992.5	TSL:2 MANE Select	c.297G>T	p.Arg99Arg	synonymous	Exon 2 of 9	ENSP00000477817.1	A0A087WTF0
	PTPDC1	ENST00000288976.3	TSL:1	c.291G>T	p.Arg97Arg	synonymous	Exon 2 of 9	ENSP00000288976.3	A2A3K4-2
	PTPDC1	ENST00000375360.7	TSL:1	c.135G>T	p.Arg45Arg	synonymous	Exon 3 of 10	ENSP00000364509.3	A2A3K4-1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.7
DANN	Benign	0.82
PhyloP100		0.081

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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.

Other links and lift over

hg19: chr9-96847585;