8-98027656-T-C

Variant names:

• chr8-98027656-T-C
• rs1002041327
• NM_002380.5:c.2183T>C

Variant summary

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

The NM_002380.5(MATN2):​c.2183T>C​(p.Met728Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: MATN2 NM_002380.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 8.02

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]

RPL30 (HGNC:10333): (ribosomal protein L30) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L30E family of ribosomal proteins. It is located in the cytoplasm. This gene is co-transcribed with the U72 small nucleolar RNA gene, which is located in its fourth intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [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, 0.861

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATN2	NM_002380.5	c.2183T>C	p.Met728Thr	missense_variant	Exon 14 of 19	ENST00000254898.7	NP_002371.3
MATN2	NM_030583.4	c.2183T>C	p.Met728Thr	missense_variant	Exon 14 of 19		NP_085072.2
MATN2	NM_001317748.2	c.2060T>C	p.Met687Thr	missense_variant	Exon 13 of 18		NP_001304677.1
MATN2	XM_005250920.3	c.1943-2806T>C		intron_variant	Intron 13 of 17		XP_005250977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MATN2	ENST00000254898.7	c.2183T>C	p.Met728Thr	missense_variant	Exon 14 of 19	1	NM_002380.5	ENSP00000254898.6
MATN2	ENST00000520016.5	c.2183T>C	p.Met728Thr	missense_variant	Exon 13 of 18	1		ENSP00000430487.1
MATN2	ENST00000521689.5	c.2183T>C	p.Met728Thr	missense_variant	Exon 14 of 19	1		ENSP00000429977.1
MATN2	ENST00000524308.5	c.2060T>C	p.Met687Thr	missense_variant	Exon 13 of 18	1		ENSP00000430221.1
MATN2	ENST00000518154.5	c.1529T>C	p.Met510Thr	missense_variant	Exon 11 of 16	1		ENSP00000429622.1
MATN2	ENST00000522025.6	c.1331T>C	p.Met444Thr	missense_variant	Exon 13 of 18	5		ENSP00000429010.1
MATN2	ENST00000521952.5	n.*25-2806T>C		intron_variant	Intron 4 of 8	5		ENSP00000429256.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461582 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727082

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 21, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2183T>C (p.M728T) alteration is located in exon 14 (coding exon 13) of the MATN2 gene. This alteration results from a T to C substitution at nucleotide position 2183, causing the methionine (M) at amino acid position 728 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.55
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.32
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.28	.;T;.;.;T
Eigen	Pathogenic	0.78
Eigen_PC	Pathogenic	0.75
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.90	D;D;D;D;.
M_CAP	Uncertain	0.13	D
MetaRNN	Pathogenic	0.86	D;D;D;D;D
MetaSVM	Uncertain	0.31	D
MutationAssessor	Uncertain	2.4	M;M;.;.;M
PrimateAI	Uncertain	0.73	T
PROVEAN	Uncertain	-3.5	D;D;D;D;D
REVEL	Pathogenic	0.84
Sift	Pathogenic	0.0	D;D;D;D;D
Sift4G	Uncertain	0.0030	D;D;D;D;D
Polyphen		1.0	D;D;.;.;D
Vest4		0.83
MutPred		0.58		Loss of catalytic residue at M728 (P = 0.0537);Loss of catalytic residue at M728 (P = 0.0537);.;.;Loss of catalytic residue at M728 (P = 0.0537);
MVP		0.95
MPC		0.82
ClinPred		0.99	D
GERP RS		5.2
Varity_R		0.83
gMVP		0.81

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: rs1002041327; hg19: chr8-99039884;