chr1-161307376-T-G

Position:

• chr1-161307376-T-G

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1 PM2 PP3 PP5_Very_Strong

The ENST00000533357.5(MPZ):​c.116A>C​(p.His39Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,252 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H39Q) has been classified as Uncertain significance.

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
• Consequence: MPZ ENST00000533357.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8
• Conservation: PhyloP100: 2.74

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 Pathogenic. Variant got 13 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 14 uncertain in ENST00000533357.5
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.755
• PP5: Variant 1-161307376-T-G is Pathogenic according to our data. Variant chr1-161307376-T-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 217232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-161307376-T-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MPZ	NM_000530.8	c.116A>C	p.His39Pro	missense_variant	2/6	ENST00000533357.5	NP_000521.2
MPZ	NM_001315491.2	c.116A>C	p.His39Pro	missense_variant	2/6		NP_001302420.1
MPZ	XM_017001321.3	c.146A>C	p.His49Pro	missense_variant	2/6		XP_016856810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MPZ	ENST00000533357.5	c.116A>C	p.His39Pro	missense_variant	2/6	1	NM_000530.8	ENSP00000432943	P1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152252 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 32

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152252 Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1 AN XY: 74378

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000756

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Oct 21, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 25, 2024	Published functional studies demonstrate a damaging effect: partial loss of function (PMID: 18337304); Not observed in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26310628, 29687021, 14711881, 17602703, 16844954, 20461396, 18337304) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Oct 24, 2022	This variant associates in multiple families with clinical features of Charcot-Marie Tooth disease. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). This variant occurs as the most likely explanation for disease in a significant number of cases, suggesting this variant is associated with disease. -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Feb 21, 2023	The MPZ c.116A>C; p.His39Pro variant (rs371856018) is reported in the literature in numerous individuals affected with Charcot-Marie-Tooth syndrome or neuropathy (Kilfoyle 2006, Sanmaneechai 2015, Shy 2004, Souayah 2007). This variant was observed to co-segregate with disease in multiple families (Kilfoyle 2006, Shy 2004, Souayah 2007), including one large family where it was observed in 10 affected individuals and was absent from 24 unaffected individuals (Kilfoyle 2006). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Based on available information, including its occurrence in a large number of affected individuals, this variant is considered to be pathogenic. References: Kilfoyle DH et al. Myelin protein zero mutation His39Pro: hereditary motor and sensory neuropathy with variable onset, hearing loss, restless legs and multiple sclerosis. J Neurol Neurosurg Psychiatry. 2006 Aug;77(8):963-6. Sanmaneechai O et al. Genotype-phenotype characteristics and baseline natural history of heritable neuropathies caused by mutations in the MPZ gene. Brain. 2015 Nov;138(Pt 11):3180-92. Shy ME et al. Phenotypic clustering in MPZ mutations. Brain. 2004 Feb;127(Pt 2):371-84. Souayah N et al. Rare myelin protein zero sequence variant in late onset CMT1B. J Neurol Sci. 2007 Dec 15;263(1-2):177-9. -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 21, 2022

The c.116A>C (p.H39P) alteration is located in exon 2 (coding exon 2) of the MPZ gene. This alteration results from a A to C substitution at nucleotide position 116, causing the histidine (H) at amino acid position 39 to be replaced by a proline (P). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been reported in multiple individuals with adult-onset demyelinating Charcot-Marie-Tooth disease type 1B and cosegregates with disease in two families (Shy, 2004; Kilfoyle, 2006; Souayah, 2007). This amino acid position is not well conserved in available vertebrate species. This alteration was found to be functionally abnormal in an assay of MPZ-mediated intercellular adhesion (Grandis, 2008). This alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Charcot-Marie-Tooth disease type 1B Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University of Leipzig Medical Center

Jun 12, 2024

Criteria applied: PS3,PM1,PS4_SUP,PM2_SUP -

MPZ-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

May 15, 2024

Variant summary: MPZ c.116A>C (p.His39Pro) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 251300 control chromosomes. c.116A>C has been reported in the literature in multiple individuals affected with MPZ-Related Disorders. These data indicate that the variant is very likely to be associated with disease. ClinVar contains an entry for this variant (Variation ID: 217232). Based on the evidence outlined above, the variant was classified as pathogenic. -

Charcot-Marie-Tooth disease, type I Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 11, 2024

This sequence change replaces histidine, which is basic and polar, with proline, which is neutral and non-polar, at codon 39 of the MPZ protein (p.His39Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Charcot-Marie-Tooth disease (CMT) (PMID: 14711881, 16844954, 17602703, 26310628). It has also been observed to segregate with disease in related individuals. This variant is also known as p.His10Pro. ClinVar contains an entry for this variant (Variation ID: 217232). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MPZ protein function. Experimental studies have shown that this missense change affects MPZ function (PMID: 18337304). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.64
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.070
CADD	Uncertain	25
DANN	Benign	0.96
DEOGEN2	Uncertain	0.54	D
Eigen	Benign	-0.12
Eigen_PC	Benign	0.080
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.63	T
M_CAP	Benign	0.023	T
MetaRNN	Pathogenic	0.76	D
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.1	M
MutationTaster	Benign	0.99	D;D;D;D
PrimateAI	Uncertain	0.56	T
PROVEAN	Uncertain	-3.5	D
REVEL	Benign	0.27
Sift	Benign	0.11	T
Sift4G	Benign	0.20	T
Polyphen		0.0020	B
Vest4		0.79
MVP		0.94
MPC		1.6
ClinPred		0.97	D
GERP RS		5.3
Varity_R		0.95
gMVP		0.98

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

LitVar

Other links and lift over

dbSNP: rs371856018; hg19: chr1-161277166;