rs121907998
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PM1PP2PP5_Very_Strong
The NM_000053.4(ATP7B):c.1934T>G(p.Met645Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000222 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. M645V) has been classified as Uncertain significance.
Frequency
Consequence
NM_000053.4 missense
Scores
Clinical Significance
Conservation
Publications
- Wilson diseaseInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Pathogenic. The variant received 11 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000053.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ATP7B | NM_000053.4 | MANE Select | c.1934T>G | p.Met645Arg | missense | Exon 6 of 21 | NP_000044.2 | ||
| ATP7B | NM_001406511.1 | c.1934T>G | p.Met645Arg | missense | Exon 7 of 22 | NP_001393440.1 | |||
| ATP7B | NM_001406512.1 | c.1934T>G | p.Met645Arg | missense | Exon 7 of 22 | NP_001393441.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ATP7B | ENST00000242839.10 | TSL:1 MANE Select | c.1934T>G | p.Met645Arg | missense | Exon 6 of 21 | ENSP00000242839.5 | ||
| ATP7B | ENST00000634844.1 | TSL:1 | c.1934T>G | p.Met645Arg | missense | Exon 6 of 21 | ENSP00000489398.1 | ||
| ATP7B | ENST00000418097.7 | TSL:1 | c.1934T>G | p.Met645Arg | missense | Exon 6 of 20 | ENSP00000393343.2 |
Frequencies
GnomAD3 genomes 0.000414 AC: 63AN: 152116Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000517 AC: 129AN: 249580 AF XY: 0.000487 show subpopulations
GnomAD4 exome AF: 0.000203 AC: 296AN: 1461584Hom.: 0 Cov.: 31 AF XY: 0.000193 AC XY: 140AN XY: 727102 show subpopulations
Age Distribution
GnomAD4 genome 0.000414 AC: 63AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74432 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Wilson disease Pathogenic:18
This missense variant replaces methionine with arginine at codon 645 of the ATP7B protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). This variant has shown to cause almost complete, out-of-frame skipping of exon 6 in mini-gene RNA assays using four different cell lines (PMID: 32284880). In compound heterozygous or homozygous HepG2 cell lines that were edited for this c.1934T>C variant using CRISPR/Cas9 technology, the amount of full length transcript was reduced by more than 70%, consistent with significantly reduced ATP7B protein expression in these cells (PMID: 32284880). This variant has been reported in over 50 individuals affected with Wilson disease (PMID: 9311736, 9482578, 9671279, 15024742, 15952988, 17300695, 17433323, 17949296, 19118915, 21832955, 22484412, 23518715, 23962630, 24706876, 32043565, 33159804). In over 30 of these individuals, this variant was reported in the compound heterozygous or homozygous state (PMID: 9482578, 15024742, 15952988, 19118915, 22484412, 23518715, 23962630, 33159804). This variant is highly prevalent among Wilson disease patients of Spanish descent and has been observed in 55% of Spanish individuals with Wilson disease (PMID: 15952988). This variant has been identified in 133/280976 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
Across a selection of available literature, the c.1934T>G (p.Met645Arg) variant has been identified in a compound heterozygous state in at least 23 patients with Wilson disease (Shah et al. 1997; Kalinsky et al. 1998; Deguti et al. 2004; Margarit at al. 2005). The p.Met645Arg variant was absent from 195 controls but is reported at a frequency of 0.00285 in the Latino population of the Exome Aggregation Consortium. The p.Met645Arg variant results in a change of a neutral nonpolar residue to a basic residue. The variant is located in trans-membrane region 1, hence this substitution is expected to disrupt the structure of the transmembrane domain. Functional studies in Sf9 cells demonstrated that the variant displayed copper uptake activity that was indistinguishable from wild type, however the variant was hyperphosphorylated compared to wild type ATP7B (Huster et al. 2012). Studies in SV40-transformed ATP7A-null cells also showed that the p.Met645Arg variant and other missense variants do not disrupt copper transport activity (Braiterman et al. 2014). The biochemical defect for this variant therefore remains to be elucidated. Based on the clinical evidence from the literature, the p.Met645Arg variant is classified as pathogenic for Wilson disease.
The ATP7B c.1934T>G (p.M645R) variant has previously been reported in the homozygous and compound heterozygous state in individuals with Wilson disease (PMID: 11093740; 9482578; 9671269; 15952988; 19118915; 20301685).
This missense variant replaces methionine with arginine at codon 645 of the ATP7B protein. Computational prediction suggests that this variant may not impact protein structure and function. This variant has shown to cause almost complete, out-of-frame skipping of exon 6 in mini-gene RNA assays using four different cell lines (PMID: 32284880). In compound heterozygous or homozygous HepG2 cell lines that were edited for this c.1934T>C variant using CRISPR/Cas9 technology, the amount of full length transcript was reduced by more than 70%, consistent with significantly reduced ATP7B protein expression in these cells (PMID: 32284880). This variant has been reported in over 50 individuals affected with Wilson disease (PMID: 9311736, 9482578, 9671279, 15024742, 15952988, 17300695, 17433323, 17949296, 19118915, 21832955, 22484412, 23518715, 23962630, 24706876, 32043565, 33159804). In over 30 of these individuals, this variant was confirmed to be in the compound heterozygous or homozygous state (PMID: 9482578, 15024742, 15952988, 19118915, 22484412, 23518715, 23962630, 33159804). This variant is highly prevalent among Wilson disease patients of Spanish descent and has been observed in 55% of Spanish individuals with Wilson disease (PMID: 15952988). This variant has been identified in 133/280976 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
This sequence change replaces methionine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 645 of the ATP7B protein (p.Met645Arg). This variant is present in population databases (rs121907998, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with Wilson disease (PMID: 9311736, 9482578, 9671269, 11093740, 15952988, 19118915, 21832955). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 3862). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt ATP7B protein function with a negative predictive value of 80%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on ATP7B function (PMID: 9311736, 22240481). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
This variant is interpreted as likely pathogenic for Wilson disease, autosomal recessive. NM_000053.4:c.1934T>G has been identified in a compound heterozygous state in multiple patients with Wilson disease (for example PMID:9482578, 9671269, 11093740, 15952988, 17949296), and is present in gnomAD at a frequency compatible with disease prevalence. Functional studies have been published, but results are contradictory. Some studies (PubMed:17919502, 24706876, 22240481) show that the variant has no functional effect. Merico et al. (PubMed:32284880) demonstrate that NM_000053.4:c.1934T>G causes 70% skipping of exon 6. Exon 6 skipping results in frameshift and stop gain, and reduced protein expression. The following ACMG Tag(s) were applied to variant interpretation: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PM3-Very Strong => For recessive disorders, detected in trans with a pathogenic variant. Criterion has been upgraded because the variant has been detected in multiple patients.
The ATP7B c.1934T>G; p.Met645Arg variant (rs121907998) has been reported in numerous individuals with Wilson disease who were compound heterozygous with another pathogenic variant (Coffey 2013, Deguti 2004, Garcia-Villarreal 2000, Kalinsky 1998, Loudianos 1998, Margarit 2005, Shah 1997). One study of a Spanish Wilson disease cohort observed this variant in 55% of affected individuals (Margarit 2005). This variant is reported in ClinVar (Variation ID: 3862) and is found in the general population with an overall allele frequency of 0.05% (133/280976 alleles) in the Genome Aggregation Database. Functional studies show the variant protein becomes hyperphosphorylated but otherwise has similar copper uptake activity as wild type ATP7B protein (Braiterman 2014, Huster 2012); therefore, the disease-causing mechanism of this variant is unclear. However, based on available information, including its prevalence in affected individuals, the p.Met645Arg variant is considered pathogenic. References: Braiterman LT et al. Distinct phenotype of a Wilson disease mutation reveals a novel trafficking determinant in the copper transporter ATP7B. Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):E1364-73. PMID: 24706876. Coffey AJ et al. A genetic study of Wilson's disease in the United Kingdom. Brain. 2013 May;136(Pt 5):1476-87. PMID: 23518715. Deguti MM et al. Wilson disease: novel mutations in the ATP7B gene and clinical correlation in Brazilian patients. Hum Mutat. 2004 Apr;23(4):398. PMID: 15024742. Garcia-Villarreal L et al. High prevalence of the very rare Wilson disease gene mutation Leu708Pro in the Island of Gran Canaria (Canary Islands, Spain): a genetic and clinical study. Hepatology. 2000 Dec;32(6):1329-36. PMID: 11093740. Huster D et al. Diverse functional properties of Wilson disease ATP7B variants. Gastroenterology. 2012 Apr;142(4):947-956.e5. PMID: 22240481. Kalinsky H et al. Novel ATP7B mutations causing Wilson disease in several Israeli ethnic groups. Hum Mutat. 1998;11(2):145-51. PMID: 9482578. Loudianos G et al. Further delineation of the molecular pathology of Wilson disease in the Mediterranean population. Hum Mutat. 1998;12(2):89-94. PMID: 9671269. Margarit E et al. Mutation analysis of Wilson disease in the Spanish population -- identification of a prevalent substitution and eight novel mutations in the ATP7B gene. Clin Genet. 2005 Jul;68(1):61-8. PMID: 15952988. Shah AB et al. Identification and analysis of mutations in the Wilson disease gene (ATP7B): population frequencies, genotype-phenotype correlation, and functional analyses. Am J Hum Genet. 1997 Aug;61(2):317-28. PMID: 9311736.
NM_000053.3(ATP7B):c.1934T>G(M645R) is a missense variant classified as likely pathogenic in the context of Wilson disease. M645R has been observed in cases with relevant disease (PMID: 23518715, 19118915, 32043565, 33159804, 15952988, 23962630). Functional assessments of this variant are available in the literature (PMID: 24706876). M645R has been observed in population frequency databases (gnomAD: AMR 0.22%). In summary, NM_000053.3(ATP7B):c.1934T>G(M645R) is a missense variant that has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
Criteria applied: PM3_STR,PS3_SUP,PP3, PS4_STR; Identified as compund heterozygous with NM_000053.4:c.3045G>A
not provided Pathogenic:3
Published functional studies demonstrate nearly complete exon-skipping when the variant was transfected into different cell lines (Merico et al., 2019); This variant is associated with the following publications: (PMID: 32043565, 31980526, 32067425, 32284880, 32154060, 15952988, 27285482, 27437191, 17919502, 27398169, 25525159, 27415407, 28856630, 9311736, 24706876, 28433111, 22692182, 23962630, 22240481, 24253677, 29482223)
PM3_VSTR, PS3
Inborn genetic diseases Pathogenic:1
The c.1934T>G (p.M645R) alteration is located in exon 6 (coding exon 6) of the ATP7B gene. This alteration results from a T to G substitution at nucleotide position 1934, causing the methionine (M) at amino acid position 645 to be replaced by an arginine (R). Based on data from the Genome Aggregation Database (gnomAD) database, the ATP7B c.1934T>G alteration was observed in 0.05% (133/280976) of total alleles studied, with a frequency of 0.23% (24/10362) in the Ashkenazi Jewish subpopulation. This mutation has been detected in many compound heterozygous individuals with Wilson Disease, some of whom had only mild symptoms (Margarit, 2005; Kalinsky, 1998; Loudianos, 1998; Shah, 1997; García-Villarreal, 2000; Peña-Quintana, 2012; Arruda, 2014). Minigene analysis of this variant in four cell lines demonstrated that this variant results in increased exon skipping compared to wildtype, with Hep2G cells compound heterozygous for this mutation expressing 15% of wild type levels and homozygous cells expressing approximately 30% (Merico, 2020). The in silico prediction for the p.M645R alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.
ATP7B-related disorder Pathogenic:1
The ATP7B c.1934T>G variant is predicted to result in the amino acid substitution p.Met645Arg. This variant has been reported in the homozygous or compound heterozygous state in several patients with Wilson disease (see for example Shah et al. 1997. PubMed ID: 9311736; Kalinsky et al.1998. PubMed ID: 9482578; Loudianos et al. 1998. PubMed ID: 9671269). Experimental studies of the effect of this variant on ATP7B transport activity are conflicting. One study observed a decrease in copper transport in lymphoblast cell lines from patients homozygous for c.1934T>G (Shah et al. 1997. PubMed ID: 9311736). In contrast, this variant apparently had no affect on transporter activity when heterologously expressed in a model insect cell line (Huster et al. 2012. PubMed ID: 22240481). Based on the collective information, particularly that from patients, we interpret the c.1934T>G variant to be pathogenic.
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at