rs557271556

Variant summary

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

The NM_001297654.2(DDR1):​c.586G>A​(p.Ala196Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,550 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

DDR1
NM_001297654.2 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.56
Variant links:
Genes affected
DDR1 (HGNC:2730): (discoidin domain receptor tyrosine kinase 1) Receptor tyrosine kinases play a key role in the communication of cells with their microenvironment. These kinases are involved in the regulation of cell growth, differentiation and metabolism. The protein encoded by this gene belongs to a subfamily of tyrosine kinase receptors with homology to Dictyostelium discoideum protein discoidin I in their extracellular domain, and that are activated by various types of collagen. Expression of this protein is restricted to epithelial cells, particularly in the kidney, lung, gastrointestinal tract, and brain. In addition, it has been shown to be significantly overexpressed in several human tumors. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2011]

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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=0.2360937).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DDR1NM_001297654.2 linkc.586G>A p.Ala196Thr missense_variant Exon 6 of 18 ENST00000376568.8 NP_001284583.1 Q08345-1A0A024RCL1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DDR1ENST00000376568.8 linkc.586G>A p.Ala196Thr missense_variant Exon 6 of 18 1 NM_001297654.2 ENSP00000365752.3 Q08345-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000406
AC:
1
AN:
246216
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
134194
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000330
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000411
AC:
6
AN:
1460550
Hom.:
0
Cov.:
32
AF XY:
0.00000688
AC XY:
5
AN XY:
726574
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000848
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.25
BayesDel_addAF
Uncertain
0.13
D
BayesDel_noAF
Uncertain
0.040
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.030
T;T;.;.;.;.;T;T;T;T;.;T;.;T;.
Eigen
Benign
0.12
Eigen_PC
Benign
0.14
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.86
D;.;.;.;.;.;D;.;.;D;.;.;.;.;D
M_CAP
Uncertain
0.089
D
MetaRNN
Benign
0.24
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.77
T
MutationAssessor
Uncertain
2.2
.;M;M;M;M;M;.;M;M;.;.;.;M;.;M
PrimateAI
Uncertain
0.55
T
PROVEAN
Benign
-1.5
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL
Benign
0.089
Sift
Benign
0.15
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Sift4G
Benign
0.10
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.13, 0.63
.;B;.;.;.;.;.;B;B;.;.;.;.;.;P
Vest4
0.56, 0.60, 0.61, 0.61, 0.61, 0.56, 0.56, 0.58, 0.59, 0.58, 0.60
MutPred
0.28
Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);.;.;Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);Gain of phosphorylation at A196 (P = 0.0623);
MVP
0.93
ClinPred
0.65
D
GERP RS
4.3
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.7
Varity_R
0.084
gMVP
0.76

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: rs557271556; hg19: chr6-30859177; API