GeneBe

rs374172497

Variant names:

Variant summary

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

The NM_002500.5(NEUROD1):​c.*654_*677delAAAAAAAAAAAAAAAAAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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: 𝑓 0.000020 ( 0 hom., cov: 0)

Consequence

NEUROD1
NM_002500.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.03

Publications

1 publications found
Variant links:
Genes affected
NEUROD1 (HGNC:7762): (neuronal differentiation 1) This gene encodes a member of the NeuroD family of basic helix-loop-helix (bHLH) transcription factors. The protein forms heterodimers with other bHLH proteins and activates transcription of genes that contain a specific DNA sequence known as the E-box. It regulates expression of the insulin gene, and mutations in this gene result in type II diabetes mellitus. [provided by RefSeq, Jul 2008]
CERKL (HGNC:21699): (ceramide kinase like) This gene was initially identified as a locus (RP26) associated with an autosomal recessive form of retinitis pigmentosa (arRP) disease. This gene encodes a protein with ceramide kinase-like domains, however, the protein does not phosphorylate ceramide and its target substrate is currently unknown. This protein may be a negative regulator of apoptosis in photoreceptor cells. Mutations in this gene cause a form of retinitis pigmentosa characterized by autosomal recessive cone and rod dystrophy (arCRD). Alternative splicing of this gene results in multiple transcript variants encoding different isoforms and non-coding transcripts.[provided by RefSeq, May 2010]
CERKL Gene-Disease associations (from GenCC):
  • CERKL-related retinopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • retinitis pigmentosa 26
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • retinitis pigmentosa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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
NEUROD1NM_002500.5 linkc.*654_*677delAAAAAAAAAAAAAAAAAAAAAAAA 3_prime_UTR_variant Exon 2 of 2 ENST00000295108.4 NP_002491.3 Q13562A0A0S2Z493
NEUROD1NR_146175.2 linkn.88+3294_88+3317delAAAAAAAAAAAAAAAAAAAAAAAA intron_variant Intron 1 of 1
NEUROD1NR_146176.2 linkn.88+3294_88+3317delAAAAAAAAAAAAAAAAAAAAAAAA intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NEUROD1ENST00000295108.4 linkc.*654_*677delAAAAAAAAAAAAAAAAAAAAAAAA 3_prime_UTR_variant Exon 2 of 2 1 NM_002500.5 ENSP00000295108.3 Q13562

Frequencies

GnomAD3 genomes
AF:
0.0000203
AC:
1
AN:
49326
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000808
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000203
AC:
1
AN:
49326
Hom.:
0
Cov.:
0
AF XY:
0.0000464
AC XY:
1
AN XY:
21530
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
13758
American (AMR)
AF:
0.00
AC:
0
AN:
2860
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
1520
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1732
South Asian (SAS)
AF:
0.000808
AC:
1
AN:
1238
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
486
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
32
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
26732
Other (OTH)
AF:
0.00
AC:
0
AN:
596
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome 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
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs374172497; hg19: chr2-182541839; API