chrX-101403984-C-G

Position:

chrX-101403984-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 6P and 8B. PM1PM5PP3_ModerateBS1BS2

The NM_000169.3(GLA):c.196G>C(p.Glu66Gln) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,203,291 control chromosomes in the GnomAD database, including 2 homozygotes. There are 49 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E66G) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.000036 ( 0 hom., 0 hem., cov: 23)

Exomes 𝑓: 0.00014 ( 2 hom. 49 hem. )

Consequence

GLA
NM_000169.3 missense, splice_region

Scores

Splicing: ADA: 0.9018

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:8B:5

Conservation

PhyloP100: 7.86

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]

GLA links:

RPL36A-HNRNPH2 (HGNC:):

RPL36A-HNRNPH2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM1

In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 9 uncertain in NM_000169.3

PM5

Other missense variant is known to change same aminoacid residue: Variant chrX-101403983-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 2689132.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Uncertain_significance=1}.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.908

BS1

Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000142 (155/1090911) while in subpopulation EAS AF= 0.00507 (153/30189). AF 95% confidence interval is 0.00441. There are 2 homozygotes in gnomad4_exome. There are 49 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 2 Mitochondrial gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLA	NM_000169.3 linkuse as main transcript	c.196G>C	p.Glu66Gln	missense_variant, splice_region_variant	2/7	ENST00000218516.4
RPL36A-HNRNPH2	NM_001199973.2 linkuse as main transcript	c.301-7952C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLA	ENST00000218516.4 linkuse as main transcript	c.196G>C	p.Glu66Gln	missense_variant, splice_region_variant	2/7	1	NM_000169.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0000356

AC:

AN:

112326

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

34504

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00111

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000115

AC:

AN:

182566

Hom.:

AF XY:

0.0000745

AC XY:

AN XY:

67110

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00152

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000142

AC:

155

AN:

1090911

Hom.:

Cov.:

AF XY:

0.000137

AC XY:

AN XY:

356565

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000284

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00507

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000218

GnomAD4 genome

AF:

0.0000356

AC:

AN:

112380

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

34568

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00111

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000302

ExAC

AF:

0.000107

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:8Benign:5

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Fabry disease

Uncertain:2Benign:4

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 03, 2022	This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 66 of the GLA protein (p.Glu66Gln). This variant is present in population databases (rs104894833, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with classic, non-classic, and late onset Fabry disease and/or hypertrophic cardiomyopathy and renal failure without accumulation of Gb-3 or lysosomal deposits reported on renal or cardiac biopsy (PMID: 1315715, 7575533, 11137837, 20505683, 22874111, 23146289, 26179544, 26456105, 27160240). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 163548). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change does not substantially affect GLA function (PMID: 22305854, 26179544). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. -
Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 15, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Likely benign, criteria provided, single submitter	clinical testing	3billion	May 22, 2022	This variant is observed at a frequency of 0.148% within East Asian subpopulation with 5 hemizygous male in gnomAD v2.1.1 dataset (BS1_S, BS2_S, total allele frequency: 0.01%). Missense variant of GLA gene is a common mechanism associated with Fabry disease (PP2_P). In silico prediction tools and conservation analysis predicted that this variant was probably damaging to the protein structure/function (PP3_P, 3CNET: 0.990, REVEL: 0.926). Therefore, this variant is classified as likely benign according to the recommendation of ACMG/AMP guideline. -

not specified

Uncertain:2Benign:1

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 05, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 09, 2023	Variant summary: GLA c.196G>C (p.Glu66Gln) results in a 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 0.0023 in 249895 control chromosomes, predominantly at a frequency of 0.008 within the Japanese subpopulation, and including at least 88 hemizygous males and 3 homozygous females (gnomAD v2, Lee_2010, jMorp database, Tadaka_2021). The observed variant frequency within the Japanese subpopulation is approximately 1.6 fold of the estimated maximal expected allele frequency for a pathogenic variant in GLA causing Fabry disease (0.005) in control chromomes, suggesting that the variant is benign. c.196G>C has been reported in the literature in sequencing studies of individuals affected with a variety of Fabry disease-related phenotypes. A comprehensive review of literature spanning over two decades identified its occurrence in patients with reported/suspected diagnosis of Fabry disease (example, Ishii_1992, Park_2009, Lee_2010, Shimotori_2007, Sakuraba_2018), cohorts of male hemodialysis patients (Doi_2012, Maruyama_2013), patients on maintenance dialysis (Nishino_2012), male ischemic stroke (Nakamura_2013, Nagamatsu_2017) and newborn screening (Hwu_2009). It has also been observed in at least one case control study of patients with chronic kidney disease in whom no association with disease progression was identified (Watanabe_2015). Examples of isolated case reports of patients with this variant include, cerebral hemorrhage (Nakamura_2010), hemodialysis (Kikumoto_2012), a male with interstitial Nephritis and no pathological or cellular characteristics of Fabry disease (Satomura_2015), a male with suspected Fabry disease due to end stage renal failure and cardiomegaly in whom no pathological characteristics of Fabry were identified (Kobayashi_2012) and Parkinsonism without classic symptoms of Fabry (Tomizawa_2015). Notably many studies ascertained above also reported this variant in patients with normal levels of lyso Gb3, a common biomarker for Fabry disease (example, Sakuraba_2018). The variant was reported in two hemizygous brothers with suspected cardiac Fabry disease (Yoshitama_2001) and also to co-segregate with the phenotype of chronic glomerulonephritis in one large Chinese family (Peng_2016). Additional reports of similar co-segregation in other kindreds will help corroborate these findings. In summary, these reports do not provide evidence for an unequivocal association of this variant with the phenotype of classic Fabry disease. At least one reported co-occurrence in cis with another pathogenic variant in the GLA gene in a male patient with classic Fabry disease has been reported (GLA c.334C>T, p.Arg112Cys), providing supporting evidence for a benign role (Ishii_1992). Several publications report experimental evidence evaluating an impact on protein function with variable findings on GLA enzyme activities in-vitro in transfected cells and patient leukocytes. The most pronounced variant effect results in less than 10% activity in some studies (example, Peng_2016, patient leukocytes),but 30%-50% of normal activity in many others (example, Park_2009, Shimotori_2007, Hwu_2009 in transfected cells). Furthermore, at least one in-vitro study evaluating kinetic parameters reported some instability at a neutral pH of 7.5 (reflective of the environment in the ER lumen) despite no impact on the enzyme kinetic properties at pH 4.5 (example, Ishii_2007). Therefore, given the wide variability in reported activities across a cross section of studies evaluated, an exact in-vivo impact of these findings on the associated pathophysiology of Fabry disease is not apparent. Eight ClinVar submitters (evaluation after 2014) have cited the variant, at-least one of whom reported other distinct and separate publications from those summarized above. These submitters reported the variant with con -
Uncertain significance, no assertion criteria provided	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 11, 2013	proposed classification - variant undergoing re-assessment, contact laboratory -

not provided

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jul 28, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 07, 2017	- -

GLA-related disorder

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 30, 2024

The GLA c.196G>C variant is predicted to result in the amino acid substitution p.Glu66Gln. This variant occurs relatively frequently in the gnomAD general population database, with a subpopulation allele frequency as high as 0.15% in East Asian individuals and 5 hemizygous individuals documented. However, it has also been identified in a large number of individuals with Fabry disease (Ishii et al. 1992. PubMed ID: 1315715; Park et al. 2009. PubMed ID: 19287194; Lee et al. 2010. PubMed ID: 20505683; Shimotori et al. 2008. PubMed ID: 18205205; Sakuraba et al. 2018. PubMed ID: 30386727) and non-classic Fabry disease, mostly with singular clinical features including kidney disease (Doi et al. 2012. PubMed ID: 22695894; Watanabe et al. 2015. PubMed ID: 24718812; Satomura et al. 2015. PubMed ID: 26179544; Kobayashi et al. 2012. PubMed ID: 23146289), stroke (Nakamura et al. 2014. PubMed ID: 23724928), hypertrophic cardiomyopathy (Oikawa et al. 2016. PubMed ID: 27160240), and among newborns with abnormal newborn screening results (Hwu et al. 2009. PubMed ID: 19621417). This variant has been reported to co-segregate with kidney disease in one family (Peng et al. 2016. PubMed ID: 26456105). Of note, affected patients harboring the p.Gly66Gln variant often have normal levels of lyso Gb3, a biomarker of Fabry disease (see for example Sakuraba et al. 2018. PubMed ID: 30386727). Analysis of alpha-galactosidase A enzyme activity has produced conflicting results, with some studies reporting less than 10% activity (Peng et al. 2016. PubMed ID: 26456105) and many others reporting 30-60% of normal activity (Park et al. 2009. PubMed ID: 19287194; Hwu et al. 2009. PubMed ID: 19621417; Shimotori et al. 2008. PubMed ID: 18205205; Sakuraba et al. 2018. PubMed ID: 30386727). We suspect that this variant may be benign; however, it is possible that this variant may contribute to Fabry disease phenotypes with incomplete penetrance. Therefore, at this time, we interpret it to be a variant of uncertain significance due to conflicting genetic and functional data. -

Cardiovascular phenotype

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 04, 2022

The p.E66Q variant (also known as c.196G>C), located in coding exon 2 of the GLA gene, results from a G to C substitution at nucleotide position 196. The glutamic acid at codon 66 is replaced by glutamine, an amino acid with highly similar properties. This alteration has been reported in an individual with classical Fabry disease; however, he was also identified to have an additional alteration in GLA (Ishii S et al. Hum Genet, 1992 Apr;89:29-32). Additionally, this alteration was detected in several individuals with concerns for late onset Fabry disease (Yoshitama T et al. Am J Cardiol, 2001 Jan;87:71-5; Nakao S et al. Kidney Int, 2003 Sep;64:801-7; Shimotori M et al. Hum Mutat, 2008 Feb;29:331; Nakamura K et al. J Hum Genet, 2010 Apr;55:259-61; Lee BH et al. J Hum Genet, 2010 Aug;55:512-7; Kobayashi M et al. Mol Genet Metab, 2012 Dec;107:711-5; Doi K et al. J Hum Genet, 2012 Sep;57:575-9; Tomizawa Y et al. Intern Med, 2015 Oct;54:2503-6; Satomura A et al. Intern Med, 2015 Jul;54:1819-24; Oikawa M et al. BMC Cardiovasc Disord, 2016 May;16:83; Sakuraba H et al. Mol Genet Metab Rep, 2018 Dec;17:73-79; Kinoshita N et al. J Stroke Cerebrovasc Dis, 2018 Dec;27:3563-3569; Kim WS et al. J Korean Med Sci, 2019 Feb;34:e63). In vitro studies showed this alteration may not impact protein function (Hwu WL et al. Hum Mutat, 2009 Oct;30:1397-405; Park JY et al. Exp Mol Med, 2009 Jan;41:1-7). Based on data from gnomAD, the C allele has an overall frequency of 0.0108% (22/204601) total alleles studied, with 5 hemizygote(s) observed. The highest observed frequency was 0.1480% (22/14865) of East Asian alleles. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

CardioboostCm

Uncertain

0.89

BayesDel_addAF

Pathogenic

0.17

BayesDel_noAF

Pathogenic

0.44

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.96

D;.

FATHMM_MKL

Pathogenic

1.0

LIST_S2

Uncertain

0.95

D;T

M_CAP

Pathogenic

0.99

MetaRNN

Pathogenic

0.89

D;D

MetaSVM

Pathogenic

0.85

MutationAssessor

Uncertain

2.8

M;.

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.59

PROVEAN

Uncertain

-2.8

D;.

REVEL

Pathogenic

0.93

Sift

Uncertain

0.0020

D;.

Sift4G

Uncertain

0.0030

D;.

Polyphen

0.99

D;.

Vest4

0.80

MutPred

0.96

Loss of ubiquitination at K67 (P = 0.1);.;

MVP

0.98

MPC

1.7

ClinPred

0.29

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.96

gMVP

0.99

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.90

dbscSNV1_RF

Pathogenic

0.79

SpliceAI score (max)

0.44

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.44

Position offset: -3

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over