rs148158093

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2

The NM_000169.3(GLA):​c.352C>T​(p.Arg118Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000605 in 1,209,304 control chromosomes in the GnomAD database, including 2 homozygotes. There are 219 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00040 ( 1 hom., 13 hem., cov: 23)
Exomes 𝑓: 0.00063 ( 1 hom. 206 hem. )

Consequence

GLA
NM_000169.3 missense

Scores

9
6
3

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:20B:3O:1

Conservation

PhyloP100: 2.23
Variant links:
Genes affected
GLA (HGNC:4296): (galactosidase alpha) This gene encodes a homodimeric glycoprotein that hydrolyses the terminal alpha-galactosyl moieties from glycolipids and glycoproteins. This enzyme predominantly hydrolyzes ceramide trihexoside, and it can catalyze the hydrolysis of melibiose into galactose and glucose. A variety of mutations in this gene affect the synthesis, processing, and stability of this enzyme, which causes Fabry disease, a rare lysosomal storage disorder that results from a failure to catabolize alpha-D-galactosyl glycolipid moieties. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PP3
MetaRNN computational evidence supports a deleterious effect, 0.752
BS2
High Hemizygotes in GnomAd4 at 13 Mitochondrial gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GLANM_000169.3 linkuse as main transcriptc.352C>T p.Arg118Cys missense_variant 2/7 ENST00000218516.4 NP_000160.1
RPL36A-HNRNPH2NM_001199973.2 linkuse as main transcriptc.301-8108G>A intron_variant NP_001186902.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GLAENST00000218516.4 linkuse as main transcriptc.352C>T p.Arg118Cys missense_variant 2/71 NM_000169.3 ENSP00000218516 P1

Frequencies

GnomAD3 genomes
AF:
0.000400
AC:
45
AN:
112545
Hom.:
1
Cov.:
23
AF XY:
0.000375
AC XY:
13
AN XY:
34711
show subpopulations
Gnomad AFR
AF:
0.0000646
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000564
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000162
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000676
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000224
AC:
41
AN:
183291
Hom.:
0
AF XY:
0.000207
AC XY:
14
AN XY:
67751
show subpopulations
Gnomad AFR exome
AF:
0.0000760
Gnomad AMR exome
AF:
0.000109
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000428
Gnomad OTH exome
AF:
0.000442
GnomAD4 exome
AF:
0.000626
AC:
687
AN:
1096759
Hom.:
1
Cov.:
30
AF XY:
0.000569
AC XY:
206
AN XY:
362157
show subpopulations
Gnomad4 AFR exome
AF:
0.000265
Gnomad4 AMR exome
AF:
0.000170
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000770
Gnomad4 OTH exome
AF:
0.000586
GnomAD4 genome
AF:
0.000400
AC:
45
AN:
112545
Hom.:
1
Cov.:
23
AF XY:
0.000375
AC XY:
13
AN XY:
34711
show subpopulations
Gnomad4 AFR
AF:
0.0000646
Gnomad4 AMR
AF:
0.000564
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000162
Gnomad4 NFE
AF:
0.000676
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000602
Hom.:
24
Bravo
AF:
0.000400
TwinsUK
AF:
0.00162
AC:
6
ALSPAC
AF:
0.000346
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000595
AC:
4
ExAC
AF:
0.000247
AC:
30
EpiCase
AF:
0.000818
EpiControl
AF:
0.000474

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:20Benign:3Other:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Fabry disease Uncertain:10Other:1
Uncertain significance, criteria provided, single submitterclinical testingVictorian Clinical Genetics Services, Murdoch Childrens Research InstituteMar 31, 2022Curated 19/3/2021: Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS - 3A. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with Fabry disease (MIM#301500). Truncating variants in the last exon have been reported with a dominant negative mechanism, while those predicted to undergo nonsense mediated decay been reported with a loss of function mechanism. Missense variants have been reported with both aforementioned mechanisms. Gain of function has also been suggested, however more evidence is required (PMID: 8878432; PMID: 31613176). (I) 0109 - This gene is associated with X-linked disease. Both males and females have been reported with Fabry disease, though the latter are more rarely reported and tend to have milder disease (OMIM, PMID: 31613176). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v3) <0.001 for a dominant condition (30 heterozygotes, 1 homozygote, 13 hemizygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v3) (4 heterozygotes, 0 homozygotes, 1 hemizygote). (I) 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 melibiase 2 domain (Pfam). (I) 0701 - Another missense variant comparable to the one identified in this case has inconclusive previous evidence for pathogenicity. p.(Arg118His) has previously been reported as a VUS in at least one publication (PMID 30477121). Alternative amino acid changes to serine, glycine, proline and leucine have not been reported in patients, however, were studied via site-directed mutagenesis and found to result in enzymatic activities ranging from 40-70% of wild-type, which is higher that 20% found for p.(Arg118Cys) (PMID: 23935525). (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been reported as a variant of uncertain significance (11x) and likely pathogenic (2x) in ClinVar. In the literature, it has been reported in both male and female patients, where the variant results in residual enzyme activities that is consistent with mild, late onset Fabry disease (PMID: 16773563; 20122163; 30569317; 31291414). However, the pathogenicity of this variant has been called into question by at least one publication by demonstrating that the variant does not segregate with Fabry disease (PMID: 25468652) and in another publication where a different variant in GLA was deemed to be causative of FD the family (PMID:28941980). Lukas et al (2013) refer to this variant's clinical phenotype as being a "variant phenotype" (PMID: 23935525). The "variant phenotype" is explained by Andrade et al (2008) as having a low level of residual alpha-galactosidase activity that protects patients from developing classic FD, however some patients may present with late onset end-organ failure (PMID: 18003767). (I) 1001 - This variant has strong functional evidence supporting abnormal protein function. Gaspar et al (2010) measured alpha-galactose activity in patient leukocytes and found that the variant conferred a reduction of enzyme activity to 35% of wild-type in 1 hemizygous male and 60%-79% of wild-type in 2 heterozygous females (PMID: 20122163). In vitro functional studies of this variant showed a reduction of enzymatic actiivities ranging between 20-29% in 2 independent studies (PMID: 1677356; 23935525). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Uncertain significance, criteria provided, single submittercurationBroad Center for Mendelian Genomics, Broad Institute of MIT and HarvardJan 22, 2020The p.Arg118Cys variant in GLA has been reported in at least 11 individuals with Fabry disease (PMID: 28596458, 16773563, 20122163, 21890869, 22551898, 28299312, 28409012, 21946453, 20110537, 25468652, 24582695, 24661928, 18830871), and has been identified in 0.044% (41/92573) of European (non-Finnish) chromosomes, including 16 hemizygotes, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs148158093). This variant has also been reported in ClinVar as a VUS by the Laboratory for Molecular Medicine, GeneDx, Invitae, Ambry Genetics, GeneReviews, and the University of Washington Medical Center and as likely pathogenic by EGL Genetic Diagnostics (Variation ID: 42454). In vitro functional studies provide some evidence that the p.Arg118Cys variant may impact protein function (PMID: 23935525, 28646478, 16773563, 25468652, 20122163). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. The phenotype of an individual hemizygous for this variant is highly specific for Fabry disease based on the classical phenotype consistent with the disease (PMID: 28596458, 16773563, 20122163, 21890869, 22551898, 28299312, 28409012, 21946453, 20110537, 25468652, 24582695, 24661928, 18830871). This variant was found in cis with another pathogenic variant, suggesting that it may not cause disease (PMID: 28941980) In summary, the clinical significance of the p.Arg118Cys variant is uncertain due to conflicting data. ACMG/AMP Criteria applied: BS1, PS3_moderate, PP4, BP2 (Richards 2015). -
Uncertain significance, criteria provided, single submitterclinical testingMGZ Medical Genetics CenterJan 18, 2022- -
Uncertain significance, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthDec 05, 2023This missense variant replaces arginine with cysteine at codon 118 of the GLA protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have shown that this variant causes partially reduced GLA enzyme activity in mammalian cells (PMID: 23935525, 16773563). This variant has been reported in individuals affected with late-onset Fabry disease (PMID: 20122163, 22551898, 25468652, 35743707) and with hypertrophic cardiomyopathy (PMID: 31291414, 32531501, Koraichi et al. 2021, DOI: 10.1016/j.acvdsp.2020.10.086). A study of 22 individuals of Portuguese and Spanish ancestry carrying this variant, including 3 homozygous females, has suggested that this variant does not appear to segregate with Fabry disease (PMID: 25468652). This variant has been observed in an individual affected with idiopathic end-stage renal failure (PMID: 31566927). His three sons and two daughters who carried this variant were asymptomatic with normal GLA enzyme activity. This variant has been identified in 48/205229 chromosomes in the general population by the Genome Aggregation Database (gnomAD) and includes 17 hemizygous observations. In summary, while this variant has been reported in individuals affected with GLA-related disorders, the role of this variant in disease cannot be determined conclusively due to the frequent variant observation in unaffected individuals. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 01, 2022This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 118 of the GLA protein (p.Arg118Cys). This variant is present in population databases (rs148158093, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with mild, atypical or late-onset Fabry disease (PMID: 16773563, 18830871, 20110537, 20122163, 21890869, 22551898, 25179549, 25468652, 29631605, 30569317, 30773290). ClinVar contains an entry for this variant (Variation ID: 42454). 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) performed at Invitae indicates that this missense variant is expected to disrupt GLA protein function. Experimental studies have shown that this missense change affects GLA function (PMID: 16773563, 23935525). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -
Uncertain significance, criteria provided, single submitterclinical testingCentre for Mendelian Genomics, University Medical Centre LjubljanaMay 09, 2019This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PP2,PP3,PP5,BP6. This variant was detected in hemizygous state. -
Uncertain significance, no assertion criteria providedclinical testingNatera, Inc.Sep 16, 2020- -
Uncertain significance, no assertion criteria providedresearchCSER _CC_NCGL, University of WashingtonAug 01, 2016Found in a female patient having exome sequencing for an unrelated indication. No known history of Fabry disease. -
not provided, no classification providedliterature onlyGeneReviews-- -
Uncertain significance, criteria provided, single submitterclinical testingGenome-Nilou LabJul 15, 2021- -
not provided Pathogenic:1Uncertain:4Benign:3
Uncertain significance, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicNov 30, 2022- -
Likely benign, no assertion criteria providedresearchGharavi Laboratory, Columbia UniversitySep 16, 2018- -
Uncertain significance, criteria provided, single submitterclinical testingBlueprint GeneticsOct 26, 2017- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2023GLA: BS2 -
Likely pathogenic, flagged submissionclinical testingEurofins Ntd Llc (ga)Jan 11, 2018- -
Uncertain significance, criteria provided, single submitterclinical testingRevvity Omics, RevvityNov 06, 2023- -
Likely benign, criteria provided, single submitterclinical testingGeneDxMay 23, 2023See Variant Classification Assertion Criteria. -
Uncertain significance, criteria provided, single submitterclinical testingClinical Genetics Laboratory, Skane University Hospital LundMay 27, 2022- -
not specified Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpSep 05, 2023Variant summary: GLA c.352C>T (p.Arg118Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00023 in 184752 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in GLA causing Fabry Disease (0.00023 vs 0.005). However, the finding of 17 hemizygous occurrences in gnomAD may be evidence against pathogenicity, although the possibility of reduced penetrance and/or subclinical cases cannot be ruled out. This variant has been found in patients predominantly of Portuguese or Spanish ancestry, with clinical features ranging from no symptoms to acute cerebrovascular disease, ischemic stroke, intracerebral hemorrhage, cerebral venous thrombosis, kidney diseases, dilated cardiomyopathy, and hypertrophic cardiomyopathy (e.g. Morais_2008, Baptista_2010, Gaspar_2010, Valbuena_2012, Rolfs _2013, Caetano_2014, Golbus_2014, Alharbi_2019, Varela_2020, Delarosa-Rodriguez_2021). In patients (harboring this variant) who presented with cardiological manifestations that are shared by Fabry disease (FD) as well as other independent cardiac phenotypes (such as DCM), a deleterious variant was also found (TPM1 D230N; Golbus_2014). Additionally, this variant has been reported in patients who did not meet clinical criteria for FD (e.g. Morais_2008, Kilarski_2015, de Greef_2016, Nowak_2019, Azevedo_2020, Stiles_2020). Furthermore, Ferreira et al (2015) reviewed the clinical, biochemical and histopathology data obtained from 22 individuals of Portuguese and Spanish ancestry carrying the R118C allele and concluded that the variant did not segregate with FD clinical phenotypes in a Mendelian fashion, but might be a modulator of the multifactorial risk of cerebrovascular disease. Additionally, co-occurrence of the variant in cis with a pathogenic variant (GLA deletion of exons 3 and 4) was reported in a multi-generational family affected with Fabry Disease, providing supporting evidence for a benign role (Barbeito-Caamano_2018). Although in vitro studies strongly suggest decreased enzymatic activity associated with this variant (Lukas_2013, Spada_2006), enzymatic evaluation in patients' blood or plasma varied from reduced enzymatic level to normal levels. Multiple submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments. The majority of submitters classified the variant as VUS (n=17), and others classified it as either likely pathogenic (n=2) or likely benign (n=2). Taken together, this variant is classified as VUS until more definitive data on genotype-phenotype associations and disease progression/natural history and burden become available. -
Uncertain significance, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineFeb 08, 2019Variant classified as Uncertain Significance - Favor Benign. The p.Arg118Cys variant in GLA has been reported in 11 individuals with classic or late-onset Fabry disease and segregated with disease in at least 2 affected family members. This variant has also been identified in at least 2 individuals with reduced a-galactosidase activity, 6 individuals who had stroke, 1 individual who had MI, 1 individual with small fiber neuropathy, 1 individual with juvenile idiopathic arthritis, 4 individuals with LVH, 1 child with HCM, 2 infants with RCM and DCM, and 3 individuals with other phenotypes (Spada 2006, Gaspar 2010, Baptista 2010, Kiesling 2014, Genoni 2011, Morais 2008, Elliott 2011, Turaca 2012, Caetano 2014, Pasqualim 2014, Colon 2017, Barajas-Colon 2017, de Greef 2016, Goncalves 2017, Kilarski 2015, Schiffmann 2017, Samuelsson 2014, Ferreira 2015). However, this variant has also been reported in 7 asymptomatic family members, including 3 homozygous females, (Ferreira 2015) and did not segregate with cardiac phenotypes in 3 affected family members of 2 different families (Golbus 2014, LMM data). This variant has been reported in ClinVar (Variation ID 42454) and has been identified in 36/90523 of European chromosomes, including 14 hemizygotes, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs148158093). GLA activity in individuals carrying this variant was reduced, but did not reach levels associated with classic Fabry disease. Similarly, in vitro functional studies showed enzyme activity of 20-29% (Spada 2006, Lukas 2013). Computational prediction tools and conservation analysis suggest that the p.Arg118Cys variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the p.Arg118Cys variant is uncertain due to conflicting data. ACMG/AMP Criteria applied: PS4_M; PVS1_Moderate; PP1; PP3; BS4. -
Cardiomyopathy Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingCHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern OntarioAug 15, 2019- -
Uncertain significance, criteria provided, single submitterclinical testingCenter for Advanced Laboratory Medicine, UC San Diego Health, University of California San DiegoJan 22, 2019- -
GLA-related disorder Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJun 10, 2024The GLA c.352C>T variant is predicted to result in the amino acid substitution p.Arg118Cys. This variant has an extensive history of conflicting literature regarding it's contribution to Fabry disease phenotypes. It has been reported in multiple individuals with late-onset Fabry disease (examples include: Spada et al. 2006. PubMed ID: 16773563; Baptista et al. 2010. PubMed ID: 20110537; Gaspar et al. 2010. PubMed ID: 20122163). However, it was also shown not to segregate with clinical, biochemical or histopathology features of Fabry disease in a large cohort, including in three phenotypically unaffected individuals who were homozygous for the c.352C>T variant (Ferreira et al. 2015. PubMed ID: 25468652). This variant has been observed in 48 of ~205,000 alleles in the gnomAD general population database including 17 hemizygous males. Enzyme analysis from patient cell lines and transient mammalian expression systems indicate that the p.Arg118Cys substitution causes a reduction in activity (<25% of wild-type; Lukas et al. 2013. PubMed ID: 23935525; Spada et al. 2006. PubMed ID: 16773563). In ClinVar, this variant has conflicting interpretations including uncertain and likely pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/42454/). An internal summary of amino acid substitution prediction programs finds conflicting predictions for the p.Arg118Cys change (Liu et al. 2016. PMID: 26555599). Taken together, it is possible that the c.352C>T allele poses an increased risk for Fabry-associated phenotypes; however, at present, this variant is classified as a variant of uncertain significance for Mendelian disease. -
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJun 29, 2022The c.352C>T (p.R118C) alteration is located in exon 2 (coding exon 2) of the GLA gene. This alteration results from a C to T substitution at nucleotide position 352, causing the arginine (R) at amino acid position 118 to be replaced by a cysteine (C). 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
0.11
CardioboostCm
Uncertain
0.12
BayesDel_addAF
Uncertain
0.072
D
BayesDel_noAF
Pathogenic
0.31
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Pathogenic
0.99
D;.
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Pathogenic
0.98
D;D
M_CAP
Pathogenic
0.80
D
MetaRNN
Pathogenic
0.75
D;D
MetaSVM
Pathogenic
0.90
D
MutationAssessor
Pathogenic
2.9
M;.
MutationTaster
Benign
0.65
N
PrimateAI
Benign
0.23
T
PROVEAN
Pathogenic
-4.7
D;.
REVEL
Pathogenic
0.69
Sift
Uncertain
0.0010
D;.
Sift4G
Uncertain
0.0020
D;.
Polyphen
0.99
D;.
Vest4
0.23
MVP
0.99
MPC
1.7
ClinPred
0.84
D
GERP RS
3.9
Varity_R
0.55
gMVP
0.91

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs148158093; hg19: chrX-100658816; COSMIC: COSV54508358; COSMIC: COSV54508358; API