2-115343841-C-A

Variant summary

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

The NM_020868.6(DPP10):​c.200C>A​(p.Thr67Asn) 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 1,459,730 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T67I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

DPP10
NM_020868.6 missense

Scores

7
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.24
Variant links:
Genes affected
DPP10 (HGNC:20823): (dipeptidyl peptidase like 10) This gene encodes a single-pass type II membrane protein that is a member of the S9B family in clan SC of the serine proteases. This protein has no detectable protease activity, most likely due to the absence of the conserved serine residue normally present in the catalytic domain of serine proteases. However, it does bind specific voltage-gated potassium channels and alters their expression and biophysical properties. Mutations in this gene have been associated with asthma. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

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=0.17644429).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DPP10NM_020868.6 linkc.200C>A p.Thr67Asn missense_variant Exon 3 of 26 ENST00000410059.6 NP_065919.3 Q8N608-1B2RCJ8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DPP10ENST00000410059.6 linkc.200C>A p.Thr67Asn missense_variant Exon 3 of 26 1 NM_020868.6 ENSP00000386565.1 Q8N608-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1459730
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
726094
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:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.078
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Uncertain
-0.040
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Benign
0.026
T;T;.;.;.;.;.
Eigen
Benign
-0.26
Eigen_PC
Benign
-0.036
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.80
T;T;T;T;T;T;T
M_CAP
Uncertain
0.099
D
MetaRNN
Benign
0.18
T;T;T;T;T;T;T
MetaSVM
Uncertain
0.12
D
MutationAssessor
Benign
1.3
.;L;.;.;.;.;.
PrimateAI
Uncertain
0.62
T
PROVEAN
Benign
-1.1
N;N;N;N;N;N;N
REVEL
Benign
0.12
Sift
Benign
0.30
T;T;T;T;T;T;T
Sift4G
Benign
0.47
T;T;T;T;T;T;T
Polyphen
0.0010
.;B;.;.;.;B;.
Vest4
0.30, 0.32, 0.29, 0.29
MutPred
0.21
.;Loss of glycosylation at T67 (P = 0.028);.;.;.;.;.;
MVP
0.60
MPC
0.19
ClinPred
0.76
D
GERP RS
5.0
Varity_R
0.25
gMVP
0.33

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: chr2-116101417; API