NM_000155.4:c.563A>G
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PP3PP5_Very_Strong
The NM_000155.4(GALT):c.563A>G(p.Gln188Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00254 in 1,614,168 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_000155.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GALT | NM_000155.4 | c.563A>G | p.Gln188Arg | missense_variant, splice_region_variant | Exon 6 of 11 | ENST00000378842.8 | NP_000146.2 | |
| GALT | NM_001258332.2 | c.236A>G | p.Gln79Arg | missense_variant, splice_region_variant | Exon 4 of 9 | NP_001245261.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GALT | ENST00000378842.8 | c.563A>G | p.Gln188Arg | missense_variant, splice_region_variant | Exon 6 of 11 | 1 | NM_000155.4 | ENSP00000368119.4 | ||
| ENSG00000258728 | ENST00000556278.1 | c.308A>G | p.Gln103Arg | missense_variant, splice_region_variant | Exon 3 of 8 | 5 | ENSP00000451792.1 |
Frequencies
GnomAD3 genomes 0.00187 AC: 284AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00143 AC: 360AN: 251466Hom.: 1 AF XY: 0.00146 AC XY: 198AN XY: 135906
GnomAD4 exome AF: 0.00261 AC: 3817AN: 1461856Hom.: 3 Cov.: 33 AF XY: 0.00250 AC XY: 1820AN XY: 727230
GnomAD4 genome 0.00187 AC: 285AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.00149 AC XY: 111AN XY: 74482
ClinVar
Submissions by phenotype
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Pathogenic:25Uncertain:1Other:1
The p.Gln188Arg variant in the GALT gene has been previously reported in at least 15 unrelated individuals with galactosemia (Reichardt et al, 1991; Singh et al 2010; and Viggiano et al 2015). All individuals were homozygous/compound heterozygous. This variant was determined to be in trans with likely pathogenic/pathogenic variants (p.Arg333Trp, p.Ser307Ter), consistent with autosomal recessive inheritance. The presence of this variant with an established/likely disease causing variant on the opposite allele increases suspicion for its pathogenicity. The p.Gln188Arg variant has been identified in 344/129182 non-Finnish European chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Well-established in vitro functional studies of this variant strongly suggest a deleterious effect to the protein that is sufficient to be disease-causing (Reichardt et al, 1991). The p.Gln188Arg variant is located in the UDP-alpha-D-glucose binding site of GALT (McCorvie et al, 2016). Other pathogenic and likely pathogenic variants have been described in this domain and cause an increase in galactose 1-phosphate uridylyltransferase aggregation due to its reduced ability to be uridylylated. Computational tools predict that this variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the c.563A>G (p.Gln188Arg) variant as pathogenic for autosomal recessive galactosemia based on the information above. [ACMG evidence codes used: PM3_strong; PS3; PP3; PM1] -
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The GALT c.563A>G, p.Gln188Arg variant (rs75391579) is the most common pathogenic GALT variant in Caucasians, and has been reported in multiple patients with galactosemia (Reichardt 1991, Viggiano 2015). Functional characterization of the variant protein indicates a significantly reduced enzymatic activity compared to wildtype (Reichardt 1991, Elsas 1994, Elsevier 1996, Lai 1999, Riehman 2001, Coelho 2014), and increased thermal instability (Elsevier 1996, Coelho 2014). This variant is reported in ClinVar (Variation ID: 3614), and is found in the general population with an overall allele frequency of 0.15% (412/282,840 alleles, including a single homozygote) in the Genome Aggregation Database. The glutamine at codon 188 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.975). Based on available information, this variant is considered to be pathogenic. References: Coelho A et al. Functional and structural impact of the most prevalent missense mutations in classic galactosemia. Mol Genet Genomic Med. 2014 2(6):484-96. PMID: 25614870. Elsas LJ et al. A common mutation associated with the Duarte galactosemia allele. Am J Hum Genet. 1994 54(6):1030-6. PMID: 8198125. Elsevier J et al. The Q188R mutation in human galactose-1-phosphate uridylyltransferase acts as a partial dominant negative. J Biol Chem. 1996 271(50):32002-7. PMID: 8943248. Lai K et al. The biochemical role of glutamine 188 in human galactose-1-phosphate uridyltransferase. J Biol Chem. 1999 274(10):6559-66. PMID: 10037750. Reichardt J et al. Molecular characterization of two galactosemia mutations: correlation of mutations with highly conserved domains in galactose-1-phosphate uridyl transferase. Am J Hum Genet. 1991 49(4):860-7. PMID: 1897530. Riehman K et al. Relationship between genotype, activity, and galactose sensitivity in yeast expressing patient alleles of human galactose-1-phosphate uridylyltransferase. J Biol Chem. 2001 276(14):10634-40. PMID: 11152465. Viggiano E et al. Clinical and molecular spectra in galactosemic patients from neonatal screening in northeastern Italy: structural and functional characterization of new variations in the galactose-1-phosphate uridyltransferase (GALT) gene. Gene. 2015 559(2):112-8. PMID: 25592817. -
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The GALT c.563A>G (p.Gln188Arg) missense variant results in the substitution of glutamine at amino acid position 188 with arginine. Across a selection of the available literature, the c.563A>G variant has been identified in a homozygous state in 37 individuals and in a compound heterozygous state in 12 individuals (PMID: 1897530; PMID: 10439960; PMID: 25592817). This variant is a well-documented pathogenic variant that accounts for >65% of alleles in individuals of northern European ancestry with GALT deficiency (PMID: 10408771; PMID: 16838075). The c.563A>G variant is reported at a frequency of 0.003249 in the European (non-Finnish) population of the Genome Aggregation Database (version 3.1.2). Functional studies suggest that the presence of the p.Gln188Arg variant results in a reduced ability to form the GALT-UMP intermediate (PMID: 10037750; PMID: 27005423). Expression of the variant in COS cells followed by enzyme activity assays showed 10% of wild-type activity, which may be due to protein misfolding and increased proteolysis as suggested by mass spectrometry studies (PMID: 1897530; PMID: 27005423). Based on the available evidence, the c.563A>G (p.Gln188Arg) variant is classified as pathogenic for galactosemia. -
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Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with Galactosemia (MIM#230400). Loss of function is a known mechanism for disease and dominant negative was also suggested by a study showing a single mutant had 15% residue function (OMIM). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamine to arginine. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (410 heterozygotes; 1 homozygote). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated UDP-alpha-D-glucose binding site within the GalP_UDP_transf functional domain (PDB). (I) 0704 - Another missense variant comparable to the one identified in this case has limited previous evidence for pathogenicity. A different variant in the same codon resulting in a changes to proline and histidine have been shown to cause galactosemia (PMID: 25681079, 29653003). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has previously been reported in many patients with galactosemia (ClinVar, PMID: 2011574, 31029175). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies show that this variant causes reduced enzyme activity (PMID: 2011574). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PM3,PP3. -
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This variant was identified as homozygous -
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ACMG classification criteria: PS3 supporting, PM3 very strong, PP3 supporting, PP4 supporting -
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NM_000155.3(GALT):c.563A>G(Q188R) is classified as pathogenic in the context of galactosemia. Sources used for classification include the following: PMID: 10439960, 1897530, 10649501, 8040766, 11152465, 8198125. Classification of NM_000155.3(GALT):c.563A>G(Q188R) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
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This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 188 of the GALT protein (p.Gln188Arg). This variant is present in population databases (rs75391579, gnomAD 0.3%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with galactosemia (PMID: 1897530, 7887417, 21188552, 25592817; internal data). This variant is also known as Q188R. ClinVar contains an entry for this variant (Variation ID: 3614). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects GALT function (PMID: 7887417, 9772178, 11152465, 25614870). 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. -
PS3, PP3, PM3_Strong -
The c.563A>G (p.Gln188Arg) missense variant in the GALT gene has been previously reported in multiple affected individuals, often in trans with other pathogenic variants (Q188P, R33W, N314D) in the GALT gene (Reichardt et al., 1991; Elsas et al., 1995a; Elsas et al., 1995b; Tran et al., 2015). In addition, the prevalence of this variant is significantly higher in affected individuals relative to unaffected individuals (OR = 99.45; 95% CI = 6.11-1617.36) and accounts for 70% of Galactosemia cases (Elsas et al., 1993; Elsas et al., 1995a; Elsas et al., 1995b; Tyfield et al., 1999). Multiple functional studies have demonstrated this variant causes reduced enzymatic activity of galactose-1-phosphate uridyltransferase (Reichardt et al., 1991; Elsas et al., 1994; Lai et al., 1999). This c.563A>G is reported at low frequency in the control population databases (Exome Sequencing Project [ESP] = 0.267%, 1000 Genomes = 0.2%, and ExAC = 0.205%). Multiple in silico algorithms predict this variant to have a deleterious effect (GERP = 4.77; CADD = 21.1; PolyPhen = 1; SIFT = 0). GALT is the only gene in which pathogenic variants are known to cause Galactosemia. Multiple reputable diagnostic laboratories have reported this variant as pathogenic in individuals affected with Galactosemia. Therefore, this collective evidence supports the classification of the c.563A>G (p.Gln188Arg) as a recessive Pathogenic variant for Galactosemia. -
Most common severe classic pathogenic variant -
The GALT c.563A>G (p.Q188R) pathogenic variant has been observed in the classic form of galactosemia (PMID: 1897530; 7887417). -
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not provided Pathogenic:5Uncertain:1
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Most common variant in Whites with classic galactosemia, occurring on approximately 70% of mutant alleles (PMID: 11261429, 15841485); Reported in homozygous individuals who had GALT activity below limits of detection (PMID: 15841485, 11261429); Published functional studies demonstrate Q188R results in significantly diminished GALT enzyme activity (PMID: 1897530); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 20222886, 9772178, 15689161, 12872845, 10439960, 27604308, 34169787, 34391645, 25087612, 25592817, 25614870, 22975760, 22995991, 10037750, 11152465, 20008339, 21228398, 1897530, 27005423, 7887417, 30987402, 29252199, 31395954, 31194252, 31954591, 31980526, 34030713, 34426522, 31589614, 30968626, 33083013, 36964972, 36099812, 36788839, 34730073, 11261429, 15841485) -
GALT: PM3:Very Strong, PM5, PP4:Moderate, PM2:Supporting, PS3:Supporting -
Galactosemia Pathogenic:3
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The p.Gln188Arg variant in GALT is the most common cause of Galactosemia, accounting for at least 50% of alleles in Caucasian and other populations and has been reported homozygously or in trans with other pathogenic alleles in more than 100 individuals with Galactosemia (Reichardt 1991, Elsas 1994, Gort 2006, Tyfield 1999, Velázquez-Aragón 2008, Özgül 2013, Viggiano 2015). This variant has also been reported in ClinVar (Variation ID: 3614). This variant has been identified in 0.265% (336/126700) of European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs75391579). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Many established functional assays have demonstrated reduced protein function of less than 1% due to the p.Gln188Arg allele (Reichardt 1991, Elsas 1995, Geeganage 1998, Tyfield 1999, Lai 1999, Riehman 2001, Coelho 2014, McCorvie 2016). Additionally, computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for Galactosemia in an autosomal recessive manner. ACMG/AMP criteria applied: PM3_VeryStrong, PS3_Moderate, PP3, PP4. -
GALT-related disorder Pathogenic:1
The GALT c.563A>G variant is predicted to result in the amino acid substitution p.Gln188Arg. This variant is one of the most common variants documented to be causative for classic galactosemia type I and is reported to account for ~70% of mutant alleles in individuals of Northern European descent (e.g., Reichardt et al. 1991. PubMed ID: 1897530; Elsas and Lai. 1998. PubMed ID: 11261429; Berry 2017. PubMed ID: 20301691). The p.Gln188 residue forms part of the GALT enzyme active site, and in multiple functional studies the p.Gln188Arg substitution has been reported to nearly abolish GALT enzyme activity (e.g., Riehman et al. 2001. PubMed ID: 11152465; Coelho et al. 2014. PubMed ID: 25614870; McCorvie et al. 2016. PubMed ID: 27005423). We, and many other outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/3614/), interpret this variant as pathogenic. -
Inborn genetic diseases Pathogenic:1
The c.563A>G (p.Q188R) alteration is located in exon 6 (coding exon 6) of the GALT gene. This alteration results from an A to G substitution at nucleotide position 563, causing the glutamine (Q) at amino acid position 188 to be replaced by an arginine (R). Based on data from gnomAD, the G allele has an overall frequency of 0.15% (412/282840) total alleles studied. The highest observed frequency was 0.27% (344/129182) of European (non-Finnish) alleles. This is a common disease-causing mutation that has been reported in the homozygous and compound heterozygous states in multiple patients with galactosemia (Fridovich-Keil, 1995; Greber-Platzer, 1997; Murphy, 1999; Viggiano, 2015; Jezela-Stanek, 2021). This amino acid position is highly conserved in available vertebrate species. Functional analysis showed ~15% of enzyme function when the p.Q188R alteration is in a heterozygous state and <1% when in a homozygous state (Elsevier, 1996; Viggiano, 2015). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at