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GeneBe

rs1340885760

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_145045.5(ODAD3):​c.1490C>T​(p.Pro497Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P497R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

ODAD3
NM_145045.5 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.563
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.04508573).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ODAD3NM_145045.5 linkuse as main transcriptc.1490C>T p.Pro497Leu missense_variant 11/13 ENST00000356392.9
ODAD3NM_001302453.1 linkuse as main transcriptc.1328C>T p.Pro443Leu missense_variant 11/13
ODAD3NM_001302454.2 linkuse as main transcriptc.1310C>T p.Pro437Leu missense_variant 9/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ODAD3ENST00000356392.9 linkuse as main transcriptc.1490C>T p.Pro497Leu missense_variant 11/131 NM_145045.5 P2A5D8V7-1
ODAD3ENST00000591179.5 linkuse as main transcriptc.1310C>T p.Pro437Leu missense_variant 9/111 A2
ODAD3ENST00000586836.5 linkuse as main transcriptc.917C>T p.Pro306Leu missense_variant 11/132 A2
ODAD3ENST00000591345.5 linkuse as main transcriptc.*1409C>T 3_prime_UTR_variant, NMD_transcript_variant 12/145

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000402
AC:
1
AN:
248736
Hom.:
0
AF XY:
0.00000739
AC XY:
1
AN XY:
135272
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000888
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461034
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
726802
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.098
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.74
CADD
Benign
2.7
DANN
Benign
0.92
DEOGEN2
Benign
0.0019
T;T;.
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.033
N
LIST_S2
Benign
0.63
T;T;T
M_CAP
Benign
0.0097
T
MetaRNN
Benign
0.045
T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
1.1
L;.;.
MutationTaster
Benign
1.0
N;N;N;N
PrimateAI
Benign
0.31
T
PROVEAN
Benign
1.6
N;.;.
REVEL
Benign
0.023
Sift
Benign
1.0
T;.;.
Sift4G
Benign
0.44
T;T;T
Polyphen
0.017
B;.;.
Vest4
0.17
MutPred
0.34
Loss of catalytic residue at P497 (P = 0.0551);.;.;
MVP
0.18
MPC
0.49
ClinPred
0.065
T
GERP RS
-6.2
Varity_R
0.026
gMVP
0.20

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1340885760; hg19: chr19-11532445; API