rs1681943

Variant names:

• chr6-63580091-C-A
• rs1681943
• NM_003463.5:c.439C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-63580091-C-A
• chr6-63580091-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_003463.5(PTP4A1):​c.439C>A​(p.Leu147Met) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PTP4A1 NM_003463.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

Genes affected

PTP4A1 (HGNC:9634): (protein tyrosine phosphatase 4A1) This gene encodes a member of a small class of prenylated protein tyrosine phosphatases (PTPs), which contain a PTP domain and a characteristic C-terminal prenylation motif. The encoded protein is a cell signaling molecule that plays regulatory roles in a variety of cellular processes, including cell proliferation and migration. The protein may also be involved in cancer development and metastasis. This tyrosine phosphatase is a nuclear protein, but may associate with plasma membrane by means of its prenylation motif. Pseudogenes related to this gene are located on chromosomes 1, 2, 5, 7, 11 and X. [provided by RefSeq, Jun 2013]

ENSG00000285976 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2662199).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTP4A1	NM_003463.5	c.439C>A	p.Leu147Met	missense_variant	Exon 6 of 6	ENST00000626021.3	NP_003454.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTP4A1	ENST00000626021.3	c.439C>A	p.Leu147Met	missense_variant	Exon 6 of 6	1	NM_003463.5	ENSP00000485687.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.094
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.070
CADD	Benign	19
DANN	Benign	0.95
DEOGEN2	Benign	0.063	T;T;.
Eigen	Benign	-0.54
Eigen_PC	Benign	-0.41
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.74	.;T;T
M_CAP	Benign	0.034	D
MetaRNN	Benign	0.27	T;T;T
MetaSVM	Uncertain	-0.27	T
MutationAssessor	Benign	1.4	L;L;.
PrimateAI	Pathogenic	0.83	D
Sift4G	Benign	0.17	.;T;T
Polyphen		0.0040	B;B;.
Vest4		0.31, 0.45
MutPred		0.42		Loss of catalytic residue at L147 (P = 0.0423);Loss of catalytic residue at L147 (P = 0.0423);.;
MVP		0.32
ClinPred		0.18	T
GERP RS		-0.66
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.6
Varity_R		0.24
gMVP		0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs1681943; hg19: chr6-64289996;