NM_001253829.2:c.113G>A

Variant names:

• chr9-94084643-G-A
• rs199730749
• NM_001253829.2:c.113G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001253829.2(PTPDC1):​c.113G>A​(p.Arg38Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000567 in 1,613,328 control chromosomes in the GnomAD database, including 1 homozygotes. 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. R38P) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00037 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00059 (1 hom.)
• Consequence: PTPDC1 NM_001253829.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.86
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.016996324).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPDC1	NM_001253829.2	c.113G>A	p.Arg38Gln	missense_variant	Exon 1 of 9	ENST00000620992.5	NP_001240758.1
PTPDC1	NM_152422.4	c.113G>A	p.Arg38Gln	missense_variant	Exon 1 of 9		NP_689635.3
PTPDC1	NM_177995.3	c.83-608G>A		intron_variant	Intron 2 of 9		NP_818931.1
PTPDC1	NM_001253830.2	c.83-608G>A		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.113G>A	p.Arg38Gln	missense_variant	Exon 1 of 9	2	NM_001253829.2	ENSP00000477817.1
PTPDC1	ENST00000288976.3	c.113G>A	p.Arg38Gln	missense_variant	Exon 1 of 9	1		ENSP00000288976.3
PTPDC1	ENST00000375360.7	c.83-608G>A		intron_variant	Intron 2 of 9	1		ENSP00000364509.3
PTPDC1	ENST00000650567.1	c.83-608G>A		intron_variant	Intron 3 of 10			ENSP00000497158.1

Frequencies

GnomAD3 genomes AF: 0.000374 AC: 57 AN: 152250 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000602

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000471 AC: 117 AN: 248212 AF XY: 0.000646

Gnomad AFR exome AF: 0.0000641

Gnomad AMR exome AF: 0.0000290

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000474

Gnomad OTH exome AF: 0.000329

GnomAD4 exome AF: 0.000587 AC: 858 AN: 1460960 Hom.: 1 Cov.: 31 AF XY: 0.000619 AC XY: 450 AN XY: 726798

African (AFR) AF: 0.0000898 AC: 3 AN: 33410

American (AMR) AF: 0.0000672 AC: 3 AN: 44660

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26094

East Asian (EAS) AF: 0.00 AC: 0 AN: 39624

South Asian (SAS) AF: 0.00154 AC: 133 AN: 86188

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53178

Middle Eastern (MID) AF: 0.000694 AC: 4 AN: 5760

European-Non Finnish (NFE) AF: 0.000600 AC: 667 AN: 1111688

Other (OTH) AF: 0.000795 AC: 48 AN: 60358

GnomAD4 genome AF: 0.000374 AC: 57 AN: 152368 Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24 AN XY: 74512

African (AFR) AF: 0.000168 AC: 7 AN: 41594

American (AMR) AF: 0.0000654 AC: 1 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4830

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000603 AC: 41 AN: 68042

Other (OTH) AF: 0.00 AC: 0 AN: 2116

Alfa AF: 0.000393 Hom.: 0

Bravo AF: 0.000348

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.000456 AC: 2

ESP6500EA AF: 0.000466 AC: 4

ExAC AF: 0.000420 AC: 51

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.000545

EpiControl AF: 0.000535

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.63	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	18
DANN	Uncertain	0.99
DEOGEN2	Benign	0.014	T;.
Eigen	Benign	-0.39
Eigen_PC	Benign	-0.24
FATHMM_MKL	Uncertain	0.76	D
LIST_S2	Benign	0.60	T;T
M_CAP	Benign	0.0071	T
MetaRNN	Benign	0.017	T;T
MetaSVM	Benign	-1.0	T
PhyloP100		2.9
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-0.64	.;N
REVEL	Benign	0.034
Sift	Uncertain	0.028	.;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		0.14	.;B
Vest4		0.27
MVP		0.28
MPC		0.19
ClinPred		0.015	T
GERP RS		3.4
PromoterAI		0.031	Neutral
gMVP		0.32
Mutation Taster		=92/8	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: rs199730749; hg19: chr9-96846925;