7-154052720-CTTTTT-CTTTTTTTT
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_130797.4(DPP6):c.-90_-88dupTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000071 ( 0 hom., cov: 6)
Exomes 𝑓: 0.0000090 ( 0 hom. )
Consequence
DPP6
NM_130797.4 5_prime_UTR
NM_130797.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0930
Publications
2 publications found
Genes affected
DPP6 (HGNC:3010): (dipeptidyl peptidase like 6) This gene encodes a single-pass type II membrane protein that is a member of the peptidase S9B family of 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. Variations in this gene may be associated with susceptibility to amyotrophic lateral sclerosis and with idiopathic ventricular fibrillation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
DPP6 Gene-Disease associations (from GenCC):
- autosomal dominant primary microcephalyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- paroxysmal familial ventricular fibrillationInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- ventricular fibrillation, paroxysmal familial, 2Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- intellectual disability, autosomal dominant 33Inheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- complex neurodevelopmental disorderInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_130797.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DPP6 | MANE Select | c.-90_-88dupTTT | 5_prime_UTR | Exon 1 of 26 | NP_570629.2 | P42658-1 | |||
| DPP6 | c.-90_-88dupTTT | 5_prime_UTR | Exon 1 of 6 | NP_001277182.1 | Q8IYG9 | ||||
| DPP6 | c.60+303723_60+303725dupTTT | intron | N/A | NP_001351426.1 | A0A994J7K0 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DPP6 | TSL:1 MANE Select | c.-90_-88dupTTT | 5_prime_UTR | Exon 1 of 26 | ENSP00000367001.3 | P42658-1 | |||
| DPP6 | TSL:1 | c.-90_-88dupTTT | 5_prime_UTR | Exon 1 of 6 | ENSP00000384393.1 | Q8IYG9 | |||
| DPP6 | TSL:1 | c.51+164997_51+164999dupTTT | intron | N/A | ENSP00000385578.1 | E9PF59 |
Frequencies
GnomAD3 genomes 0.00000707 AC: 1AN: 141506Hom.: 0 Cov.: 6 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
141506
Hom.:
Cov.:
6
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000903 AC: 9AN: 997090Hom.: 0 Cov.: 0 AF XY: 0.0000124 AC XY: 6AN XY: 483752 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
9
AN:
997090
Hom.:
Cov.:
0
AF XY:
AC XY:
6
AN XY:
483752
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
17964
American (AMR)
AF:
AC:
0
AN:
14152
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11304
East Asian (EAS)
AF:
AC:
0
AN:
10550
South Asian (SAS)
AF:
AC:
1
AN:
55272
European-Finnish (FIN)
AF:
AC:
1
AN:
11000
Middle Eastern (MID)
AF:
AC:
0
AN:
2654
European-Non Finnish (NFE)
AF:
AC:
7
AN:
839296
Other (OTH)
AF:
AC:
0
AN:
34898
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.286
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000707 AC: 1AN: 141506Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 68400 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
141506
Hom.:
Cov.:
6
AF XY:
AC XY:
0
AN XY:
68400
show subpopulations
African (AFR)
AF:
AC:
0
AN:
38700
American (AMR)
AF:
AC:
0
AN:
14352
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3370
East Asian (EAS)
AF:
AC:
0
AN:
4668
South Asian (SAS)
AF:
AC:
0
AN:
4450
European-Finnish (FIN)
AF:
AC:
0
AN:
7828
Middle Eastern (MID)
AF:
AC:
0
AN:
290
European-Non Finnish (NFE)
AF:
AC:
0
AN:
65016
Other (OTH)
AF:
AC:
1
AN:
1944
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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