NM_005401.5:c.3252A>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005401.5(PTPN14):​c.3252A>T​(p.Glu1084Asp) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. E1084E) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Consequence

PTPN14
NM_005401.5 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0750
Variant links:
Genes affected
PTPN14 (HGNC:9647): (protein tyrosine phosphatase non-receptor type 14) 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 N-terminal noncatalytic domain similar to that of band 4.1 superfamily cytoskeleton-associated proteins, which suggested the membrane or cytoskeleton localization of this protein. It appears to regulate lymphatic development in mammals, and a loss of function mutation has been found in a kindred with a lymphedema-choanal atresia. [provided by RefSeq, Sep 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22153899).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PTPN14NM_005401.5 linkc.3252A>T p.Glu1084Asp missense_variant Exon 17 of 19 ENST00000366956.10 NP_005392.2 Q15678A8K6H6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTPN14ENST00000366956.10 linkc.3252A>T p.Glu1084Asp missense_variant Exon 17 of 19 1 NM_005401.5 ENSP00000355923.4 Q15678
PTPN14ENST00000543945 linkc.*2528A>T 3_prime_UTR_variant Exon 16 of 18 5 ENSP00000443330.1 E2J9M0

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
52
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
Benign
-0.099
T
BayesDel_noAF
Benign
-0.38
CADD
Benign
15
DANN
Benign
0.96
DEOGEN2
Benign
0.19
T
Eigen
Benign
-1.1
Eigen_PC
Benign
-0.96
FATHMM_MKL
Benign
0.72
D
LIST_S2
Benign
0.85
T
M_CAP
Benign
0.064
D
MetaRNN
Benign
0.22
T
MetaSVM
Benign
-0.83
T
MutationAssessor
Benign
0.27
N
PrimateAI
Pathogenic
0.80
T
PROVEAN
Benign
-0.81
N
REVEL
Benign
0.25
Sift
Benign
0.38
T
Sift4G
Benign
0.39
T
Polyphen
0.0
B
Vest4
0.26
MutPred
0.38
Gain of disorder (P = 0.3183);
MVP
0.40
MPC
0.28
ClinPred
0.15
T
GERP RS
-0.93
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.17
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1135352; hg19: chr1-214542819; API