1-168701098-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001937.5(DPT):āc.458A>Gā(p.Tyr153Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000547 in 1,461,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0 ( 0 hom., cov: 31)
Exomes š: 0.0000055 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DPT
NM_001937.5 missense
NM_001937.5 missense
Scores
3
12
4
Clinical Significance
Conservation
PhyloP100: 5.14
Genes affected
DPT (HGNC:3011): (dermatopontin) Dermatopontin is an extracellular matrix protein with possible functions in cell-matrix interactions and matrix assembly. The protein is found in various tissues and many of its tyrosine residues are sulphated. Dermatopontin is postulated to modify the behavior of TGF-beta through interaction with decorin. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.752
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPT | NM_001937.5 | c.458A>G | p.Tyr153Cys | missense_variant | 3/4 | ENST00000367817.4 | NP_001928.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DPT | ENST00000367817.4 | c.458A>G | p.Tyr153Cys | missense_variant | 3/4 | 1 | NM_001937.5 | ENSP00000356791.3 | ||
ENSG00000285622 | ENST00000650631.1 | n.858A>G | non_coding_transcript_exon_variant | 8/9 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152176Hom.: 0 Cov.: 31 FAILED QC
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GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251350Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135830
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GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461562Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727106
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GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152176Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74334
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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 | May 03, 2023 | The c.458A>G (p.Y153C) alteration is located in exon 3 (coding exon 3) of the DPT gene. This alteration results from a A to G substitution at nucleotide position 458, causing the tyrosine (Y) at amino acid position 153 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of phosphorylation at Y153 (P = 0.0469);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
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