GeneBe

rs3831274

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004969.4(IDE):​c.1740-201_1740-190delACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000312 in 320,100 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000031 ( 0 hom. )

Consequence

IDE
NM_004969.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.969

Publications

1 publications found
Variant links:
Genes affected
IDE (HGNC:5381): (insulin degrading enzyme) This gene encodes a zinc metallopeptidase that degrades intracellular insulin, and thereby terminates insulins activity, as well as participating in intercellular peptide signalling by degrading diverse peptides such as glucagon, amylin, bradykinin, and kallidin. The preferential affinity of this enzyme for insulin results in insulin-mediated inhibition of the degradation of other peptides such as beta-amyloid. Deficiencies in this protein's function are associated with Alzheimer's disease and type 2 diabetes mellitus but mutations in this gene have not been shown to be causitive for these diseases. This protein localizes primarily to the cytoplasm but in some cell types localizes to the extracellular space, cell membrane, peroxisome, and mitochondrion. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants have been described but have not been experimentally verified.[provided by RefSeq, Sep 2009]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IDENM_004969.4 linkc.1740-201_1740-190delACACACACACAC intron_variant Intron 14 of 24 ENST00000265986.11 NP_004960.2 P14735-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IDEENST00000265986.11 linkc.1740-201_1740-190delACACACACACAC intron_variant Intron 14 of 24 1 NM_004969.4 ENSP00000265986.6 P14735-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000312
AC:
1
AN:
320100
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
167342
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
9968
American (AMR)
AF:
0.00
AC:
0
AN:
14358
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
10208
East Asian (EAS)
AF:
0.00
AC:
0
AN:
22536
South Asian (SAS)
AF:
0.00
AC:
0
AN:
26638
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
21742
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1418
European-Non Finnish (NFE)
AF:
0.00000515
AC:
1
AN:
194106
Other (OTH)
AF:
0.00
AC:
0
AN:
19126
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs3831274; hg19: chr10-94239367; API