chr17-17997528-G-C

Variant names:

• chr17-17997528-G-C
• rs201211532
• NM_031294.4:c.893G>C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_031294.4(DRC3):​c.893G>C​(p.Arg298Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DRC3 NM_031294.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.84

Genes affected

DRC3 (HGNC:25384): (dynein regulatory complex subunit 3) Located in axoneme. [provided by Alliance of Genome Resources, Apr 2022]

ATPAF2 (HGNC:18802): (ATP synthase mitochondrial F1 complex assembly factor 2) This gene encodes an assembly factor for the F(1) component of the mitochondrial ATP synthase. This protein binds specifically to the F1 alpha subunit and is thought to prevent this subunit from forming nonproductive homooligomers during enzyme assembly. This gene is located within the Smith-Magenis syndrome region on chromosome 17. An alternatively spliced transcript variant has been described, but its biological validity has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.8

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRC3	NM_031294.4	c.893G>C	p.Arg298Pro	missense_variant	Exon 9 of 14	ENST00000399187.6	NP_112584.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRC3	ENST00000399187.6	c.893G>C	p.Arg298Pro	missense_variant	Exon 9 of 14	1	NM_031294.4	ENSP00000382140.1
DRC3	ENST00000399182.5	c.893G>C	p.Arg298Pro	missense_variant	Exon 9 of 13	1		ENSP00000382136.1
DRC3	ENST00000584166.5	c.893G>C	p.Arg298Pro	missense_variant	Exon 10 of 14	5		ENSP00000462661.1
DRC3	ENST00000583171.5	n.*91+4439G>C		intron_variant	Intron 1 of 5	3		ENSP00000464101.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.040
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.30	T;T;.;.
Eigen	Pathogenic	0.73
Eigen_PC	Uncertain	0.66
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.78	T;.;.;T
M_CAP	Uncertain	0.087	D
MetaRNN	Pathogenic	0.80	D;D;D;D
MetaSVM	Uncertain	-0.21	T
PrimateAI	Uncertain	0.49	T
PROVEAN	Pathogenic	-6.3	D;D;.;D
REVEL	Uncertain	0.41
Sift	Uncertain	0.0030	D;D;.;D
Sift4G	Uncertain	0.0090	D;D;D;D
Polyphen		1.0	D;D;D;D
Vest4		0.83
MutPred		0.50		Gain of glycosylation at R298 (P = 0.0229);Gain of glycosylation at R298 (P = 0.0229);Gain of glycosylation at R298 (P = 0.0229);Gain of glycosylation at R298 (P = 0.0229);
MVP		0.87
MPC		0.85
ClinPred		0.99	D
GERP RS		4.6
Varity_R		0.94
gMVP		0.64

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: rs201211532; hg19: chr17-17900842;