6-30893089-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001297654.2(DDR1):​c.1121C>A​(p.Pro374Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

DDR1
NM_001297654.2 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.05239594).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DDR1NM_001297654.2 linkc.1121C>A p.Pro374Gln missense_variant Exon 9 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.1121C>A p.Pro374Gln missense_variant Exon 9 of 18 1 NM_001297654.2 ENSP00000365752.3 Q08345-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000800
AC:
2
AN:
250026
Hom.:
0
AF XY:
0.0000148
AC XY:
2
AN XY:
135282
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000881
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460130
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
726434
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
ExAC
AF:
0.00000824
AC:
1
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.073
BayesDel_addAF
Benign
-0.090
T
BayesDel_noAF
Benign
-0.37
CADD
Benign
5.9
DANN
Benign
0.82
DEOGEN2
Benign
0.11
T;.;.;.;.;T;T;.;.;T;.;T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.050
N
LIST_S2
Benign
0.61
.;.;.;.;.;.;.;.;.;.;T;.
M_CAP
Benign
0.031
D
MetaRNN
Benign
0.052
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
1.1
L;L;L;L;L;L;L;.;L;.;L;.
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-0.57
N;N;N;N;N;N;N;N;N;.;N;N
REVEL
Benign
0.20
Sift
Benign
0.55
T;T;T;T;T;T;T;T;T;.;T;T
Sift4G
Benign
0.67
T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.026
B;.;.;.;.;B;B;.;.;.;B;B
Vest4
0.22
MutPred
0.23
Loss of glycosylation at S373 (P = 0.061);Loss of glycosylation at S373 (P = 0.061);Loss of glycosylation at S373 (P = 0.061);Loss of glycosylation at S373 (P = 0.061);Loss of glycosylation at S373 (P = 0.061);Loss of glycosylation at S373 (P = 0.061);Loss of glycosylation at S373 (P = 0.061);.;Loss of glycosylation at S373 (P = 0.061);Loss of glycosylation at S373 (P = 0.061);Loss of glycosylation at S373 (P = 0.061);.;
MVP
0.53
ClinPred
0.052
T
GERP RS
-6.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.028
gMVP
0.34

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

LitVar

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

Other links and lift over

dbSNP: rs200571528; hg19: chr6-30860866; API