chr16-15643829-CAAGA-C
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The ENST00000674888.1(NDE1):n.-139_-136delGAAA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 156,950 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 0 hom. )
Consequence
NDE1
ENST00000674888.1 non_coding_transcript_exon
ENST00000674888.1 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.525
Publications
0 publications found
Genes affected
NDE1 (HGNC:17619): (nudE neurodevelopment protein 1) This gene encodes a member of the nuclear distribution E (NudE) family of proteins. The encoded protein is localized at the centrosome and interacts with other centrosome components as part of a multiprotein complex that regulates dynein function. This protein plays an essential role in microtubule organization, mitosis and neuronal migration. Mutations in this gene cause lissencephaly 4, a disorder characterized by lissencephaly, severe brain atrophy, microcephaly, and severe cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]
NDE1 Gene-Disease associations (from GenCC):
- lissencephaly 4Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
- hydranencephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- microlissencephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- NDE1-related microhydranencephalyInheritance: Unknown, AR Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), 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 |
---|---|---|---|---|---|---|---|---|
NDE1 | NM_001143979.2 | c.-261_-258delGAAA | 5_prime_UTR_variant | Exon 1 of 10 | NP_001137451.1 | |||
NDE1 | XM_006720897.5 | c.-43_-40delGAAA | 5_prime_UTR_variant | Exon 1 of 8 | XP_006720960.1 | |||
NDE1 | XM_047434258.1 | c.-43_-40delGAAA | 5_prime_UTR_variant | Exon 1 of 8 | XP_047290214.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDE1 | ENST00000396355.5 | c.-261_-258delGAAA | 5_prime_UTR_variant | Exon 1 of 10 | 1 | ENSP00000379643.1 | ||||
NDE1 | ENST00000674888.1 | n.-139_-136delGAAA | non_coding_transcript_exon_variant | Exon 1 of 10 | ENSP00000501936.1 | |||||
NDE1 | ENST00000674888.1 | n.-139_-136delGAAA | 5_prime_UTR_variant | Exon 1 of 10 | ENSP00000501936.1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 151898Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
19
AN:
151898
Hom.:
Cov.:
32
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: 0.000198 AC: 1AN: 5052Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 2980 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
5052
Hom.:
AF XY:
AC XY:
0
AN XY:
2980
show subpopulations
African (AFR)
AF:
AC:
0
AN:
12
American (AMR)
AF:
AC:
0
AN:
20
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
68
East Asian (EAS)
AF:
AC:
0
AN:
14
South Asian (SAS)
AF:
AC:
0
AN:
1676
European-Finnish (FIN)
AF:
AC:
0
AN:
264
Middle Eastern (MID)
AF:
AC:
0
AN:
14
European-Non Finnish (NFE)
AF:
AC:
1
AN:
2728
Other (OTH)
AF:
AC:
0
AN:
256
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 AF: 0.000125 AC: 19AN: 151898Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74174 show subpopulations
GnomAD4 genome
AF:
AC:
19
AN:
151898
Hom.:
Cov.:
32
AF XY:
AC XY:
8
AN XY:
74174
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41348
American (AMR)
AF:
AC:
0
AN:
15248
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
5174
South Asian (SAS)
AF:
AC:
0
AN:
4812
European-Finnish (FIN)
AF:
AC:
0
AN:
10568
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
18
AN:
67970
Other (OTH)
AF:
AC:
1
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lissencephaly, Recessive Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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