8-98032293-C-T

Variant names:

• chr8-98032293-C-T
• NM_002380.5:c.2557C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002380.5(MATN2):​c.2557C>T​(p.Pro853Ser) 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. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MATN2 NM_002380.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.11

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11559895).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATN2	NM_002380.5	c.2557C>T	p.Pro853Ser	missense_variant	Exon 16 of 19	ENST00000254898.7	NP_002371.3
MATN2	NM_030583.4	c.2557C>T	p.Pro853Ser	missense_variant	Exon 16 of 19		NP_085072.2
MATN2	NM_001317748.2	c.2434C>T	p.Pro812Ser	missense_variant	Exon 15 of 18		NP_001304677.1
MATN2	XM_005250920.3	c.2143C>T	p.Pro715Ser	missense_variant	Exon 15 of 18		XP_005250977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MATN2	ENST00000254898.7	c.2557C>T	p.Pro853Ser	missense_variant	Exon 16 of 19	1	NM_002380.5	ENSP00000254898.6
MATN2	ENST00000520016.5	c.2557C>T	p.Pro853Ser	missense_variant	Exon 15 of 18	1		ENSP00000430487.1
MATN2	ENST00000521689.5	c.2557C>T	p.Pro853Ser	missense_variant	Exon 16 of 19	1		ENSP00000429977.1
MATN2	ENST00000524308.5	c.2434C>T	p.Pro812Ser	missense_variant	Exon 15 of 18	1		ENSP00000430221.1
MATN2	ENST00000518154.5	c.1903C>T	p.Pro635Ser	missense_variant	Exon 13 of 16	1		ENSP00000429622.1
MATN2	ENST00000522025.6	c.1705C>T	p.Pro569Ser	missense_variant	Exon 15 of 18	5		ENSP00000429010.1
MATN2	ENST00000521952.5	n.*225C>T		non_coding_transcript_exon_variant	Exon 6 of 9	5		ENSP00000429256.1
MATN2	ENST00000521952.5	n.*225C>T		3_prime_UTR_variant	Exon 6 of 9	5		ENSP00000429256.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 06, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2557C>T (p.P853S) alteration is located in exon 16 (coding exon 15) of the MATN2 gene. This alteration results from a C to T substitution at nucleotide position 2557, causing the proline (P) at amino acid position 853 to be replaced by a serine (S). 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	Benign	0.082
BayesDel_addAF	Benign	-0.021	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	16
DANN	Benign	0.86
DEOGEN2	Benign	0.023	.;T;.;.;T
Eigen	Benign	-0.51
Eigen_PC	Benign	-0.42
FATHMM_MKL	Benign	0.21	N
LIST_S2	Benign	0.78	T;T;T;T;.
M_CAP	Benign	0.029	D
MetaRNN	Benign	0.12	T;T;T;T;T
MetaSVM	Benign	-0.65	T
MutationAssessor	Benign	0.63	N;N;.;.;N
PrimateAI	Benign	0.38	T
PROVEAN	Benign	0.020	N;N;N;N;N
REVEL	Benign	0.18
Sift	Benign	0.11	T;T;T;T;T
Sift4G	Benign	0.075	T;T;T;T;T
Polyphen		0.041	B;B;.;.;B
Vest4		0.094
MutPred		0.16		Gain of phosphorylation at P853 (P = 0.0668);Gain of phosphorylation at P853 (P = 0.0668);.;.;Gain of phosphorylation at P853 (P = 0.0668);
MVP		0.77
MPC		0.20
ClinPred		0.086	T
GERP RS		5.0
Varity_R		0.049
gMVP		0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr8-99044521;