17-80058885-C-G

Variant names:

• chr17-80058885-C-G
• rs387907093
• NM_017950.4:c.1345C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_017950.4(CCDC40):​c.1345C>G​(p.Arg449Gly) 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. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC40 NM_017950.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0210

Genes affected

CCDC40 (HGNC:26090): (coiled-coil domain 40 molecular ruler complex subunit) This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

ENSG00000289689 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.28720948).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC40	NM_017950.4	c.1345C>G	p.Arg449Gly	missense_variant	Exon 9 of 20	ENST00000397545.9	NP_060420.2
CCDC40	NM_001243342.2	c.1345C>G	p.Arg449Gly	missense_variant	Exon 9 of 18		NP_001230271.1
CCDC40	NM_001330508.2	c.1345C>G	p.Arg449Gly	missense_variant	Exon 9 of 11		NP_001317437.1
LOC124904074	XR_007065931.1	n.906G>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC40	ENST00000397545.9	c.1345C>G	p.Arg449Gly	missense_variant	Exon 9 of 20	5	NM_017950.4	ENSP00000380679.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Primary ciliary dyskinesia Uncertain:1

Sep 27, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with glycine at codon 449 of the CCDC40 protein (p.Arg449Gly). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and glycine. This variant has not been reported in the literature in individuals with CCDC40-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	12
DANN	Benign	0.93
DEOGEN2	Uncertain	0.51	.;D;.
Eigen	Benign	-0.94
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.032	N
LIST_S2	Benign	0.77	T;T;T
M_CAP	Uncertain	0.10	D
MetaRNN	Benign	0.29	T;T;T
MetaSVM	Benign	-0.85	T
MutationAssessor	Uncertain	2.5	M;M;M
PrimateAI	Benign	0.22	T
PROVEAN	Uncertain	-4.2	D;D;D
REVEL	Benign	0.15
Sift	Uncertain	0.013	D;D;D
Sift4G	Uncertain	0.0080	D;T;D
Polyphen		0.73	.;P;.
Vest4		0.39
MutPred		0.26		Loss of catalytic residue at R449 (P = 0.0507);Loss of catalytic residue at R449 (P = 0.0507);Loss of catalytic residue at R449 (P = 0.0507);
MVP		0.24
MPC		0.51
ClinPred		0.56	D
GERP RS		-9.0
Varity_R		0.12
gMVP		0.15

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

Other links and lift over

dbSNP: rs387907093; hg19: chr17-78032684;