NM_145045.5:c.1695_1697delGGA
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PM4_Supporting
The NM_145045.5(ODAD3):c.1695_1697delGGA(p.Glu565del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,554 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
ODAD3
NM_145045.5 disruptive_inframe_deletion
NM_145045.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.27
Publications
1 publications found
Genes affected
ODAD3 (HGNC:28303): (outer dynein arm docking complex subunit 3) This gene encodes a protein containing coiled-coil domains. The encoded protein functions in outer dynein arm assembly and is required for motile cilia function. Mutations in this gene result in primary ciliary dyskinesia. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]
ODAD3 Gene-Disease associations (from GenCC):
- primary ciliary dyskinesia 30Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P
- primary ciliary dyskinesiaInheritance: 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 1 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_145045.5. Strenght limited to Supporting due to length of the change: 1aa.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_145045.5. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ODAD3 | NM_145045.5 | MANE Select | c.1695_1697delGGA | p.Glu565del | disruptive_inframe_deletion | Exon 13 of 13 | NP_659482.3 | ||
| ODAD3 | NM_001302453.1 | c.1533_1535delGGA | p.Glu511del | disruptive_inframe_deletion | Exon 13 of 13 | NP_001289382.1 | A5D8V7-2 | ||
| ODAD3 | NM_001302454.2 | c.1515_1517delGGA | p.Glu505del | disruptive_inframe_deletion | Exon 11 of 11 | NP_001289383.1 | K7EN59 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ODAD3 | ENST00000356392.9 | TSL:1 MANE Select | c.1695_1697delGGA | p.Glu565del | disruptive_inframe_deletion | Exon 13 of 13 | ENSP00000348757.3 | A5D8V7-1 | |
| ODAD3 | ENST00000591179.5 | TSL:1 | c.1515_1517delGGA | p.Glu505del | disruptive_inframe_deletion | Exon 11 of 11 | ENSP00000466800.1 | K7EN59 | |
| ODAD3 | ENST00000861507.1 | c.1593_1595delGGA | p.Glu531del | disruptive_inframe_deletion | Exon 12 of 12 | ENSP00000531566.1 |
Frequencies
GnomAD3 genomes 0.0000197 AC: 3AN: 151932Hom.: 0 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
151932
Hom.:
Cov.:
30
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GnomAD2 exomes AF: 0.0000362 AC: 9AN: 248366 AF XY: 0.0000445 show subpopulations
GnomAD2 exomes
AF:
AC:
9
AN:
248366
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461622Hom.: 0 AF XY: 0.0000124 AC XY: 9AN XY: 727116 show subpopulations
GnomAD4 exome
AF:
AC:
16
AN:
1461622
Hom.:
AF XY:
AC XY:
9
AN XY:
727116
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
6
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
3
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
53386
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
7
AN:
1111786
Other (OTH)
AF:
AC:
0
AN:
60386
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.484
Heterozygous variant carriers
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Allele balance
Age Distribution
Exome Het
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Age
GnomAD4 genome 0.0000197 AC: 3AN: 151932Hom.: 0 Cov.: 30 AF XY: 0.0000404 AC XY: 3AN XY: 74170 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
151932
Hom.:
Cov.:
30
AF XY:
AC XY:
3
AN XY:
74170
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41356
American (AMR)
AF:
AC:
3
AN:
15242
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5164
South Asian (SAS)
AF:
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10590
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67976
Other (OTH)
AF:
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
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1
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Allele balance
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ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Primary ciliary dyskinesia 30 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
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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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