8-97931078-G-C

Variant names:

• chr8-97931078-G-C
• rs757584045
• NM_002380.5:c.268G>C

Variant summary

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

The NM_002380.5(MATN2):​c.268G>C​(p.Gly90Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MATN2 NM_002380.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.08

Genes affected

MATN2 (HGNC:6908): (matrilin 2) This gene encodes a member of the von Willebrand factor A domain containing protein family. This family of proteins is thought to be involved in the formation of filamentous networks in the extracellular matrices of various tissues. This protein contains five von Willebrand factor A domains. The specific function of this gene has not yet been determined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATN2	NM_002380.5	c.268G>C	p.Gly90Arg	missense_variant	Exon 3 of 19	ENST00000254898.7	NP_002371.3
MATN2	NM_030583.4	c.268G>C	p.Gly90Arg	missense_variant	Exon 3 of 19		NP_085072.2
MATN2	NM_001317748.2	c.268G>C	p.Gly90Arg	missense_variant	Exon 3 of 18		NP_001304677.1
MATN2	XM_005250920.3	c.268G>C	p.Gly90Arg	missense_variant	Exon 3 of 18		XP_005250977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MATN2	ENST00000254898.7	c.268G>C	p.Gly90Arg	missense_variant	Exon 3 of 19	1	NM_002380.5	ENSP00000254898.6
MATN2	ENST00000520016.5	c.268G>C	p.Gly90Arg	missense_variant	Exon 2 of 18	1		ENSP00000430487.1
MATN2	ENST00000521689.5	c.268G>C	p.Gly90Arg	missense_variant	Exon 3 of 19	1		ENSP00000429977.1
MATN2	ENST00000524308.5	c.268G>C	p.Gly90Arg	missense_variant	Exon 3 of 18	1		ENSP00000430221.1
MATN2	ENST00000522025.6	c.-115+538G>C		intron_variant	Intron 2 of 17	5		ENSP00000429010.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.45
BayesDel_addAF	Uncertain	0.085	D
BayesDel_noAF	Benign	-0.12
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.40	.;T;.;T
Eigen	Benign	0.17
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.94	D;D;D;.
M_CAP	Uncertain	0.15	D
MetaRNN	Uncertain	0.67	D;D;D;D
MetaSVM	Uncertain	0.14	D
MutationAssessor	Uncertain	2.6	M;M;M;M
PrimateAI	Uncertain	0.64	T
PROVEAN	Pathogenic	-6.2	D;D;D;D
REVEL	Uncertain	0.56
Sift	Uncertain	0.011	D;D;D;D
Sift4G	Uncertain	0.025	D;D;D;D
Polyphen		0.020	B;B;.;B
Vest4		0.42
MutPred		0.78		Loss of stability (P = 0.1562);Loss of stability (P = 0.1562);Loss of stability (P = 0.1562);Loss of stability (P = 0.1562);
MVP		0.91
MPC		0.30
ClinPred		0.88	D
GERP RS		4.8
Varity_R		0.26
gMVP		0.88

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: rs757584045; hg19: chr8-98943306;