chr6-30892329-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001297654.2(DDR1):​c.886C>A​(p.Arg296Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

DDR1
NM_001297654.2 missense

Scores

10
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.63
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 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DDR1NM_001297654.2 linkc.886C>A p.Arg296Ser missense_variant Exon 8 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.886C>A p.Arg296Ser missense_variant Exon 8 of 18 1 NM_001297654.2 ENSP00000365752.3 Q08345-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1421866
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
702732
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.30
BayesDel_addAF
Uncertain
0.16
D
BayesDel_noAF
Uncertain
-0.010
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.21
T;.;.;.;.;T;T;.;.;T;.;T
Eigen
Uncertain
0.37
Eigen_PC
Uncertain
0.37
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Benign
0.85
.;.;.;.;.;.;.;.;.;.;T;.
M_CAP
Benign
0.062
D
MetaRNN
Uncertain
0.48
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.63
T
MutationAssessor
Benign
1.4
L;L;L;L;L;L;L;.;L;.;L;.
PrimateAI
Uncertain
0.76
T
PROVEAN
Benign
-2.2
N;N;N;N;N;N;N;N;N;.;N;N
REVEL
Uncertain
0.30
Sift
Uncertain
0.0040
D;D;D;D;D;D;D;D;D;.;D;D
Sift4G
Benign
0.080
T;T;T;T;T;T;T;T;T;T;T;D
Polyphen
0.92
P;.;.;.;.;P;P;.;.;.;D;D
Vest4
0.40
MutPred
0.41
Loss of MoRF binding (P = 0.015);Loss of MoRF binding (P = 0.015);Loss of MoRF binding (P = 0.015);Loss of MoRF binding (P = 0.015);Loss of MoRF binding (P = 0.015);Loss of MoRF binding (P = 0.015);Loss of MoRF binding (P = 0.015);.;Loss of MoRF binding (P = 0.015);Loss of MoRF binding (P = 0.015);Loss of MoRF binding (P = 0.015);.;
MVP
0.84
ClinPred
0.83
D
GERP RS
4.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.61
gMVP
0.70

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-30860106; API