chr1-161305924-A-C

Position:

• chr1-161305924-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 6P and 1B. PM1 PM2 PP5_Moderate BP4

The NM_000530.8(MPZ):​c.699T>G​(p.Ser233Arg) 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. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: MPZ NM_000530.8 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:3
• Conservation: PhyloP100: -0.915

Genes affected

MPZ (HGNC:7225): (myelin protein zero) This gene is specifically expressed in Schwann cells of the peripheral nervous system and encodes a type I transmembrane glycoprotein that is a major structural protein of the peripheral myelin sheath. The encoded protein contains a large hydrophobic extracellular domain and a smaller basic intracellular domain, which are essential for the formation and stabilization of the multilamellar structure of the compact myelin. Mutations in this gene are associated with autosomal dominant form of Charcot-Marie-Tooth disease type 1 (CMT1B) and other polyneuropathies, such as Dejerine-Sottas syndrome (DSS) and congenital hypomyelinating neuropathy (CHN). A recent study showed that two isoforms are produced from the same mRNA by use of alternative in-frame translation termination codons via a stop codon readthrough mechanism. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM1: In a chain Myelin protein P0 (size 218) in uniprot entity MYP0_HUMAN there are 268 pathogenic changes around while only 9 benign (97%) in NM_000530.8
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-161305924-A-C is Pathogenic according to our data. Variant chr1-161305924-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 374017.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.3216121). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPZ	NM_000530.8	c.699T>G	p.Ser233Arg	missense_variant	6/6	ENST00000533357.5
MPZ	NM_001315491.2	c.699T>G	p.Ser233Arg	missense_variant	6/6
MPZ	XM_017001321.3	c.675+184T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPZ	ENST00000533357.5	c.699T>G	p.Ser233Arg	missense_variant	6/6	1	NM_000530.8	P1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, single submitter

Submissions by phenotype

Tremor;C0587246:Limb muscle weakness;C4021727:EMG: neuropathic changes Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Sep 23, 2015

- -

Roussy-Lévy syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2016

This variant was classified as: Likely pathogenic. -

Sensorimotor neuropathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Sep 23, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.69
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
CADD	Benign	14
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.44	T;D
Eigen	Benign	-0.67
Eigen_PC	Benign	-0.71
FATHMM_MKL	Benign	0.31	N
LIST_S2	Benign	0.66	T;T
M_CAP	Uncertain	0.16	D
MetaRNN	Benign	0.32	T;T
MetaSVM	Uncertain	-0.24	T
MutationAssessor	Benign	0.69	N;.
MutationTaster	Benign	0.99	D;D;D;N
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-0.81	N;D
REVEL	Uncertain	0.53
Sift	Uncertain	0.0030	D;D
Sift4G	Benign	0.15	T;T
Polyphen		0.99	D;.
Vest4		0.65
MutPred		0.35		Loss of phosphorylation at S233 (P = 0.0108);.;
MVP		0.92
MPC		0.62
ClinPred		0.90	D
GERP RS		-4.1
Varity_R		0.46
gMVP		0.46

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: rs1057518839; hg19: chr1-161275714;