NM_004393.6:c.5G>T

Variant names:

• chr3-49510539-G-T
• rs781269339
• NM_004393.6:c.5G>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_004393.6(DAG1):​c.5G>T​(p.Arg2Met) 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. 14/22 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. R2K) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DAG1 NM_004393.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.87
• Publications: 1 publications found

Genes affected

DAG1 (HGNC:2666): (dystroglycan 1) This gene encodes dystroglycan, a central component of dystrophin-glycoprotein complex that links the extracellular matrix and the cytoskeleton in the skeletal muscle. The encoded preproprotein undergoes O- and N-glycosylation, and proteolytic processing to generate alpha and beta subunits. Certain mutations in this gene are known to cause distinct forms of muscular dystrophy. Alternative splicing results in multiple transcript variants, all encoding the same protein. [provided by RefSeq, Nov 2015]

DAG1 Gene-Disease associations (from GenCC):

• autosomal recessive limb-girdle muscular dystrophy type 2P

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Genomics England PanelApp, Orphanet
• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• muscular dystrophy-dystroglycanopathy, type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• isolated asymptomatic elevation of creatine phosphokinase

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2742558).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAG1	NM_004393.6	c.5G>T	p.Arg2Met	missense_variant	Exon 2 of 3	ENST00000308775.7	NP_004384.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAG1	ENST00000308775.7	c.5G>T	p.Arg2Met	missense_variant	Exon 2 of 3	1	NM_004393.6	ENSP00000312435.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.052	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	23
DANN	Benign	0.94
DEOGEN2	Benign	0.31	T;T;T;T;T;T;T;.;.;.;.;.;T;.;.
Eigen	Benign	-0.17
Eigen_PC	Benign	-0.017
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.41	T;T;.;.;.;.;.;T;T;T;T;T;T;.;.
M_CAP	Benign	0.034	D
MetaRNN	Benign	0.27	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N;.;N;N;N;N;N;.;.;.;.;.;.;.;.
PhyloP100		2.9
PrimateAI	Uncertain	0.53	T
PROVEAN	Benign	-0.24	N;N;N;N;N;N;N;N;N;N;N;N;N;D;D
REVEL	Benign	0.12
Sift	Uncertain	0.0080	D;D;D;D;D;D;D;D;D;D;D;D;D;.;.
Sift4G	Benign	0.077	T;T;T;T;T;T;T;T;T;.;T;T;T;.;.
Polyphen		0.34	B;.;B;B;B;B;B;.;.;.;.;.;.;.;.
Vest4		0.53
MutPred		0.26		Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);Gain of glycosylation at S4 (P = 0.0069);
MVP		0.50
MPC		0.72
ClinPred		0.60	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Varity_R		0.078
gMVP		0.61
Mutation Taster		=92/8	polymorphism

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

Other links and lift over

dbSNP: rs781269339; hg19: chr3-49547972;