NM_015448.3:c.467T>G

Variant names:

• chr10-101608897-T-G
• NM_015448.3:c.467T>G

Variant summary

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

The NM_015448.3(DPCD):​c.467T>G​(p.Leu156Trp) 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. 13/17 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. L156S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: DPCD NM_015448.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

Genes affected

DPCD (HGNC:24542): (deleted in primary ciliary dyskinesia homolog (mouse)) This gene in mouse encodes a protein that may be involved in the generation and maintenance of ciliated cells. In mouse, expression of this gene increases during ciliated cell differentiation, and disruption of this gene has been linked to primary ciliary dyskinesia. [provided by RefSeq, Jul 2016]

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=0.2051169).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPCD	NM_015448.3	c.467T>G	p.Leu156Trp	missense_variant	Exon 5 of 6	ENST00000370151.9	NP_056263.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPCD	ENST00000370151.9	c.467T>G	p.Leu156Trp	missense_variant	Exon 5 of 6	1	NM_015448.3	ENSP00000359170.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	6.5
DANN	Benign	0.93
DEOGEN2	Benign	0.011	T;T
Eigen	Benign	-0.54
Eigen_PC	Benign	-0.65
FATHMM_MKL	Benign	0.31	N
LIST_S2	Benign	0.34	T;.
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.21	T;T
MetaSVM	Benign	-0.97	T
PROVEAN	Benign	-0.73	.;N
REVEL	Benign	0.023
Sift	Pathogenic	0.0	.;D
Vest4		0.31
MutPred		0.27		Gain of disorder (P = 0.0081);Gain of disorder (P = 0.0081);
MVP		0.51
ClinPred		0.85	D
GERP RS		-0.55

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-103368654;