chr1-202153828-A-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002832.4(PTPN7):āc.614T>Gā(p.Val205Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000264 in 1,613,024 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00016 ( 0 hom., cov: 32)
Exomes š: 0.00027 ( 1 hom. )
Consequence
PTPN7
NM_002832.4 missense
NM_002832.4 missense
Scores
2
11
4
Clinical Significance
Conservation
PhyloP100: 5.40
Genes affected
PTPN7 (HGNC:9659): (protein tyrosine phosphatase non-receptor type 7) 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 gene is preferentially expressed in a variety of hematopoietic cells, and is an early response gene in lymphokine stimulated cells. The non-catalytic N-terminus of this PTP can interact with MAP kinases and suppress the MAP kinase activities. This PTP was shown to be involved in the regulation of T cell antigen receptor (TCR) signaling, which was thought to function through dephosphorylating the molecules related to MAP kinase pathway. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN7 | NM_002832.4 | c.614T>G | p.Val205Gly | missense_variant | 7/10 | ENST00000691036.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN7 | ENST00000691036.1 | c.614T>G | p.Val205Gly | missense_variant | 7/10 | NM_002832.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152062Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000147 AC: 37AN: 251374Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135870
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GnomAD4 exome AF: 0.000274 AC: 401AN: 1460962Hom.: 1 Cov.: 31 AF XY: 0.000279 AC XY: 203AN XY: 726886
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GnomAD4 genome AF: 0.000164 AC: 25AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74278
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.929T>G (p.V310G) alteration is located in exon 7 (coding exon 7) of the PTPN7 gene. This alteration results from a T to G substitution at nucleotide position 929, causing the valine (V) at amino acid position 310 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;.
REVEL
Pathogenic
Sift
Benign
T;T;T;.
Sift4G
Benign
T;T;T;T
Polyphen
P;.;.;.
Vest4
MVP
MPC
0.77
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at