rs139586631

Variant names:

• chr9-94084583-C-G
• rs139586631
• NM_001253829.2:c.53C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-94084583-C-G
• chr9-94084583-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001253829.2(PTPDC1):​c.53C>G​(p.Ser18Cys) variant causes a missense 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. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S18F) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: PTPDC1 NM_001253829.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.895
• Publications: 1 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15419695).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPDC1	NM_001253829.2	c.53C>G	p.Ser18Cys	missense_variant	Exon 1 of 9	ENST00000620992.5	NP_001240758.1
PTPDC1	NM_152422.4	c.53C>G	p.Ser18Cys	missense_variant	Exon 1 of 9		NP_689635.3
PTPDC1	NM_177995.3	c.83-668C>G		intron_variant	Intron 2 of 9		NP_818931.1
PTPDC1	NM_001253830.2	c.83-668C>G		intron_variant	Intron 2 of 9		NP_001240759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPDC1	ENST00000620992.5	c.53C>G	p.Ser18Cys	missense_variant	Exon 1 of 9	2	NM_001253829.2	ENSP00000477817.1
PTPDC1	ENST00000288976.3	c.53C>G	p.Ser18Cys	missense_variant	Exon 1 of 9	1		ENSP00000288976.3
PTPDC1	ENST00000375360.7	c.83-668C>G		intron_variant	Intron 2 of 9	1		ENSP00000364509.3
PTPDC1	ENST00000650567.1	c.83-668C>G		intron_variant	Intron 3 of 10			ENSP00000497158.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.011	T;.
Eigen	Benign	-0.16
Eigen_PC	Benign	-0.22
FATHMM_MKL	Benign	0.27	N
LIST_S2	Benign	0.69	T;T
M_CAP	Benign	0.0069	T
MetaRNN	Benign	0.15	T;T
MetaSVM	Benign	-1.0	T
PhyloP100		0.90
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-0.70	.;N
REVEL	Benign	0.055
Sift	Uncertain	0.0050	.;D
Sift4G	Benign	0.096	T;T
Polyphen		0.92	.;P
Vest4		0.33
MutPred		0.26		Loss of methylation at R23 (P = 0.0704);Loss of methylation at R23 (P = 0.0704);
MVP		0.30
MPC		0.42
ClinPred		0.84	D
GERP RS		3.9
PromoterAI		-0.031	Neutral
gMVP		0.63
Mutation Taster		=91/9	polymorphism

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

Other links and lift over

dbSNP: rs139586631; hg19: chr9-96846865;