6-129250127-G-C

Variant names:

• chr6-129250127-G-C
• NM_000426.4:c.1798G>C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_000426.4(LAMA2):​c.1798G>C​(p.Gly600Arg) 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LAMA2 NM_000426.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.08

Genes affected

LAMA2 (HGNC:6482): (laminin subunit alpha 2) Laminin, an extracellular protein, is a major component of the basement membrane. It is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. It is composed of three subunits, alpha, beta, and gamma, which are bound to each other by disulfide bonds into a cross-shaped molecule. This gene encodes the alpha 2 chain, which constitutes one of the subunits of laminin 2 (merosin) and laminin 4 (s-merosin). Mutations in this gene have been identified as the cause of congenital merosin-deficient muscular dystrophy. Two transcript variants encoding different proteins have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.891

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAMA2	NM_000426.4	c.1798G>C	p.Gly600Arg	missense_variant	Exon 13 of 65	ENST00000421865.3	NP_000417.3
LAMA2	NM_001079823.2	c.1798G>C	p.Gly600Arg	missense_variant	Exon 13 of 64		NP_001073291.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMA2	ENST00000421865.3	c.1798G>C	p.Gly600Arg	missense_variant	Exon 13 of 65	5	NM_000426.4	ENSP00000400365.2
LAMA2	ENST00000618192.5	c.1798G>C	p.Gly600Arg	missense_variant	Exon 13 of 66	5		ENSP00000480802.2
LAMA2	ENST00000617695.5	c.1798G>C	p.Gly600Arg	missense_variant	Exon 13 of 64	5		ENSP00000481744.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.70
BayesDel_addAF	Benign	-0.042	T
BayesDel_noAF	Benign	-0.30
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.071	.;T;T
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.86	D;D;D
M_CAP	Benign	0.032	D
MetaRNN	Pathogenic	0.89	D;D;D
MetaSVM	Benign	-0.68	T
MutationAssessor	Pathogenic	3.1	.;.;M
PrimateAI	Uncertain	0.54	T
PROVEAN	Pathogenic	-6.6	.;.;D
REVEL	Uncertain	0.40
Sift	Benign	0.031	.;.;D
Polyphen		1.0	.;.;D
Vest4		0.68
MutPred		0.93		Loss of catalytic residue at P596 (P = 0.0966);Loss of catalytic residue at P596 (P = 0.0966);Loss of catalytic residue at P596 (P = 0.0966);
MVP		0.76
MPC		0.51
ClinPred		1.0	D
GERP RS		5.7
Varity_R		0.89
gMVP		0.89

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-129571272;