rs1060501320

Positions:

• chr19-11422589-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000356392.9(ODAD3):​c.1316A>G​(p.Lys439Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. K439K) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ODAD3 ENST00000356392.9 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 0.300

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.094031215).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODAD3	NM_145045.5	c.1316A>G	p.Lys439Arg	missense_variant	10/13	ENST00000356392.9	NP_659482.3
ODAD3	NM_001302453.1	c.1154A>G	p.Lys385Arg	missense_variant	10/13		NP_001289382.1
ODAD3	NM_001302454.2	c.1136A>G	p.Lys379Arg	missense_variant	8/11		NP_001289383.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODAD3	ENST00000356392.9	c.1316A>G	p.Lys439Arg	missense_variant	10/13	1	NM_145045.5	ENSP00000348757	P2
ODAD3	ENST00000591179.5	c.1136A>G	p.Lys379Arg	missense_variant	8/11	1		ENSP00000466800	A2
ODAD3	ENST00000586836.5	c.743A>G	p.Lys248Arg	missense_variant	10/13	2		ENSP00000467429	A2
ODAD3	ENST00000591345.5	c.*1235A>G		3_prime_UTR_variant, NMD_transcript_variant	11/14	5		ENSP00000467313

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Inborn genetic diseases Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 22, 2023

The c.1316A>G (p.K439R) alteration is located in exon 10 (coding exon 10) of the CCDC151 gene. This alteration results from a A to G substitution at nucleotide position 1316, causing the lysine (K) at amino acid position 439 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Primary ciliary dyskinesia 30 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 27, 2016

This sequence change replaces lysine with arginine at codon 439 of the CCDC151 protein (p.Lys439Arg). The lysine residue is moderately conserved and there is a small physicochemical difference between lysine and arginine. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a CCDC151-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: (SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). The arginine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies. In summary, this variant is a novel missense change that is not predicted to affect protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.94
DEOGEN2	Benign	0.0063	T;T;.
Eigen	Benign	-0.72
Eigen_PC	Benign	-0.82
FATHMM_MKL	Benign	0.034	N
LIST_S2	Benign	0.63	T;T;T
M_CAP	Benign	0.0071	T
MetaRNN	Benign	0.094	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.2	M;.;.
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-1.2	N;.;.
REVEL	Benign	0.012
Sift	Benign	0.039	D;.;.
Sift4G	Benign	0.14	T;T;T
Polyphen		0.28	B;.;.
Vest4		0.094
MutPred		0.13		Loss of ubiquitination at K439 (P = 0.0141);.;.;
MVP		0.29
MPC		0.36
ClinPred		0.14	T
GERP RS		2.0
Varity_R		0.049
gMVP		0.12

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs1060501320; hg19: chr19-11533257;