chrX-101398432-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_000169.3(GLA):​c.937G>T​(p.Asp313Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00378 in 1,207,947 control chromosomes in the GnomAD database, including 10 homozygotes. There are 1,531 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity,other (no stars).

Frequency

Genomes: 𝑓 0.0031 ( 1 hom., 104 hem., cov: 23)
Exomes 𝑓: 0.0038 ( 9 hom. 1427 hem. )

Consequence

GLA
NM_000169.3 missense

Scores

4
8
5

Clinical Significance

Conflicting classifications of pathogenicity; other criteria provided, conflicting classifications U:4B:20O:2

Conservation

PhyloP100: 0.136
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]
RPL36A-HNRNPH2 (HGNC:48349): (RPL36A-HNRNPH2 readthrough) This locus represents naturally occurring read-through transcription between the neighboring ribosomal protein L36a and heterogeneous nuclear ribonucleoprotein H2 (H') genes on chromosome X. The read-through transcript produces a protein with similarity to the protein encoded by the upstream locus, ribosomal protein L36a. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Jan 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.021395475).
BP6
Variant X-101398432-C-A is Benign according to our data. Variant chrX-101398432-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity, other]. Clinvar id is 10738.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=3, Benign=9, Likely_benign=11, other=2}. Variant chrX-101398432-C-A is described in Lovd as [Benign]. Variant chrX-101398432-C-A is described in Lovd as [Likely_pathogenic]. Variant chrX-101398432-C-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00314 (350/111368) while in subpopulation NFE AF= 0.00528 (280/53077). AF 95% confidence interval is 0.00477. There are 1 homozygotes in gnomad4. There are 104 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 104 Mitochondrial gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GLANM_000169.3 linkc.937G>T p.Asp313Tyr missense_variant Exon 6 of 7 ENST00000218516.4 NP_000160.1 P06280Q53Y83

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GLAENST00000218516.4 linkc.937G>T p.Asp313Tyr missense_variant Exon 6 of 7 1 NM_000169.3 ENSP00000218516.4 P06280
RPL36A-HNRNPH2ENST00000409170.3 linkc.300+2975C>A intron_variant Intron 4 of 4 4 ENSP00000386655.4 H7BZ11

Frequencies

GnomAD3 genomes
AF:
0.00314
AC:
350
AN:
111314
Hom.:
1
Cov.:
23
AF XY:
0.00310
AC XY:
104
AN XY:
33516
show subpopulations
Gnomad AFR
AF:
0.000719
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00153
Gnomad ASJ
AF:
0.00643
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00230
Gnomad FIN
AF:
0.000505
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00527
Gnomad OTH
AF:
0.00401
GnomAD3 exomes
AF:
0.00303
AC:
556
AN:
183499
Hom.:
2
AF XY:
0.00352
AC XY:
239
AN XY:
67935
show subpopulations
Gnomad AFR exome
AF:
0.000760
Gnomad AMR exome
AF:
0.00201
Gnomad ASJ exome
AF:
0.00681
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00252
Gnomad FIN exome
AF:
0.000625
Gnomad NFE exome
AF:
0.00443
Gnomad OTH exome
AF:
0.00419
GnomAD4 exome
AF:
0.00384
AC:
4215
AN:
1096579
Hom.:
9
Cov.:
30
AF XY:
0.00394
AC XY:
1427
AN XY:
361981
show subpopulations
Gnomad4 AFR exome
AF:
0.000455
Gnomad4 AMR exome
AF:
0.00205
Gnomad4 ASJ exome
AF:
0.00624
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00327
Gnomad4 FIN exome
AF:
0.000790
Gnomad4 NFE exome
AF:
0.00432
Gnomad4 OTH exome
AF:
0.00328
GnomAD4 genome
AF:
0.00314
AC:
350
AN:
111368
Hom.:
1
Cov.:
23
AF XY:
0.00310
AC XY:
104
AN XY:
33580
show subpopulations
Gnomad4 AFR
AF:
0.000717
Gnomad4 AMR
AF:
0.00153
Gnomad4 ASJ
AF:
0.00643
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00230
Gnomad4 FIN
AF:
0.000505
Gnomad4 NFE
AF:
0.00528
Gnomad4 OTH
AF:
0.00396
Alfa
AF:
0.00467
Hom.:
212
Bravo
AF:
0.00285
TwinsUK
AF:
0.00243
AC:
9
ALSPAC
AF:
0.00554
AC:
16
ESP6500AA
AF:
0.000522
AC:
2
ESP6500EA
AF:
0.00431
AC:
29
ExAC
AF:
0.00333
AC:
404
EpiCase
AF:
0.00469
EpiControl
AF:
0.00504

ClinVar

Significance: Conflicting classifications of pathogenicity; other
Submissions summary: Uncertain:4Benign:20Other:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Fabry disease Uncertain:3Benign:6Other:1
May 28, 2019
Mendelics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Mar 11, 2015
CSER _CC_NCGL, University of Washington
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: research

- -

Dec 27, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: other
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- pseudodeficiency allele

-
CeMIA
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.937G>T (p.Asp313Tyr) variant, located in exon 6 of the GLA gene, has been previously reported to be associated with Fabry disease (PMID: 20122163, 23393592, 26993117, 7504405), however this variant does not lead to severe organ manifestations as seen in genotypes known to be causal for classical FD (PMID: 27059467). Functional studies support that the variant renders the protein unstable at neutral pH resulting in a pseudodeficiency in plasma, but the enzyme was stable at lysosomal pH, which prompts further investigation to detect a second, causative mutation (PMID: 14635108). The variant was identified in seventeen individuals (7 hemizygous males, 10 heterozygous females), in which only thirteen (6 hemizygous males, 7 heterozygous females) were affected with Fabry disease. The presentation of the disease in the patients indicates that the mutation results in a milder phenotype, with later onset of symptoms. Bioinformatic analysis by SIFT and PolyPhen2 algorithms predicted this mutation as deleterious and probably damaging, respectively. It has been detected in 0.304% alleles worldwide (gnomAD database) and its allele frequency is higher than that expected for Fabry disease. Taking all the above into account and according to ACMG Guidelines (Criteria: PM1, PP2, PP3, BS1, BP5) the variant has contradictory interpretation of pathogenicity, therefore is considered as variant of uncertain significance. -

Jan 01, 2019
Institute of Human Genetics, University of Leipzig Medical Center
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 23, 2020
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 01, 2013
OMIM
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: literature only

- -

May 18, 2021
Genome-Nilou Lab
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 16, 2018
Color Diagnostics, LLC DBA Color Health
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Uncertain:1Benign:4Other:1
Jun 29, 2017
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 03, 2015
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The D313Y variant listed below is associated with pseudodeficiency for alpha-galactosidase A activity. D313Y reduces the in vitro activity of the alpha-galactosidase A enzyme to approximately 60-70% of normal. The presence of the D313Y variant does not cause Fabry disease [Froissart et al. (2003) Mol. Genet. Metab. 80 (3):307-14 (PMID: 14680977); Niemann et al. (2013) JIMD Rep 7 :99-102 (PMID: 23430502)].; This variant is associated with the following publications: (PMID: 32246457, 32109691, 32281532, 30477121, 31860127, 31291414, 30830284, 29227985, 28703315, 28988177, 29037082, 28299312, 28276057, 27600940, 29044343, 25382311, 27153395, 26993117, 7504405, 20110537, 23393592, 23935525, 18057066, 14680977, 23430502, 22773828, 18297328, 14635108, 24356988, 22537551, 23219219, 25078086, 21896204, 20122163, 16773563) -

Aug 12, 2024
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Apr 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

GLA: BP2, BP5, BS3:Supporting, BS1 -

Aug 22, 2018
Eurofins Ntd Llc (ga)
Significance: other
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles).

Nov 10, 2023
Revvity Omics, Revvity
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not specified Benign:4
Aug 02, 2012
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

p.Asp313Tyr in exon 6 of GLA: This variant is not expected to have clinical sign ificance for cardiomyopathy since it has been identified in 0.4% (29/6728) of Eu ropean American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS/; dbSNP rs28935490). It has been rep orted in patients with clinical manifestations ranging from classic Fabry diseas e to isolated HCM (Eng 1993, Blaydon 2001, Sachdev 2002, Froissart 2003, Yasuda 2003, Morita 2006, Monserrat 2007) and while cell culture studies showed that th e mutant GLA protein retains ~60% of the normal activity, the p.Asp313Tyr varian t renders the protein unstable at neutral pH resulting in a pseudodeficiency in plasma (Yasuda 2003). In males with classic Fabry disease, it usually occurs wit h a second GLA variant (Eng 1993, Yasuda 2003), and is highly likely insufficien t to cause classic Fabry disease in isolation. -

Jul 29, 2016
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 14, 2024
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: GLA c.937G>T (p.Asp313Tyr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0038 in 1210097 control chromosomes, predominantly at a frequency of 0.0044 within the Non-Finnish European subpopulation in the gnomAD database (v4), including 5 homozygotes and 1278 hemizygotes. This frequency is slightly lower than estimated for a pathogenic variant in GLA causing Fabry Disease (0.0038 vs 0.005) however the presence of a high number of hemizygotes suggests a generally benign role for the variant. c.937G>T has been observed in large phenotypic range of patients, from clinically normal to classic Fabry disease patients, including patients with cardiac, renal and cerebrovascular manifestations. Co-occurrences with other pathogenic variant(s) have been reported (GLA c.1232G>A, p.Gly411Asp; GLA c.334C>T, p.Arg112Cys; GLA c.514T>G, p.Cys172Gly; GLA c.811G>A, p.Gly271Ser; GLA c.835C>G , p.Gln279Glu), providing supporting evidence for a benign role. Functional studies have shown that Asp313Tyr does not disrupt enzyme structure, has >90% residual enzyme activity and is stable at lysosomal pH (4.5) (Yasuda_2003). Overall, functional studies suggest that the Asp313Tyr variant is a functional polymorphism rather than a disease-causing variant. Several studies reported the variant to be associated with a risk of neurologic involvement, particularly late-onset cerebrovascular disease, white matter lesions and small fiber neuropathy (e.g. Brouns_2010, Lenders_2010, Effraimidis_2020, Von Cossel_2021). In summary, based on the evidence outlined above, though the Asp313Tyr variant might be associated with a risk for late-onset neurologic manifestations, it does not cause Fabry disease. The following publications have been ascertained in the context of this evaluation (PMID: 25078086, 20110537, 29044343, 11668641, 20360539, 23219219, 32246457, 7504405, 14680977, 20122163, 9452111, 29037082, 28988177, 23393592, 26415523, 23430502, 29530533, 24829596, 29631605, 33543778, 14635108, 27832731, 32109691, 28276057, 35971858). ClinVar contains an entry for this variant (Variation ID: 10738). Based on the evidence outlined above, the variant was classified as benign. -

-
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Hypertrophic cardiomyopathy Benign:3
Jul 26, 2017
Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sep 29, 2022
Cohesion Phenomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sudden unexplained death Benign:1
Mar 27, 2015
Agnes Ginges Centre for Molecular Cardiology, Centenary Institute
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: research

The GLA Asp313Tyr variant has been previously reported to be associated with Fabry disease and observed in isolated HCM cases, however this variant is often identified in combination with another variant which is able to explain the disease phenotype (Eng et al., 1993; Sachdev B et al., 2002; Yasuda M et al., 2003; Monserrat L et al., 2007). The population frequency in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/) is 0.003 alleles (275/87762); and the frequency in the European (non-Finnish) sub-population is 0.004 (211/48000). We have identified this variant in a 16 yo boy who had a sudden cardiac arrest with no pre-morbid diagnosis and Greek ethnicity. Post-mortem examination was unremarkable and there is no family history of any cardiac disease. Based on the frequency of the GLA Asp313Tyr variant in 0.4% of the population, we do not expect this variant to cause disease in isolation. We therefore classify this variant as "likely benign". -

Cardiomyopathy Benign:1
Apr 19, 2023
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Cardiovascular phenotype Benign:1
Jan 11, 2018
Ambry Genetics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Uncertain
0.070
CADD
Benign
16
DANN
Uncertain
0.98
DEOGEN2
Pathogenic
0.98
D;.
FATHMM_MKL
Uncertain
0.77
D
LIST_S2
Uncertain
0.88
D;D
M_CAP
Pathogenic
0.90
D
MetaRNN
Benign
0.021
T;T
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Uncertain
2.5
M;.
PrimateAI
Benign
0.34
T
PROVEAN
Uncertain
-3.2
D;.
REVEL
Uncertain
0.61
Sift
Uncertain
0.0010
D;.
Sift4G
Pathogenic
0.0010
D;.
Polyphen
1.0
D;.
Vest4
0.24
MVP
0.99
MPC
1.9
ClinPred
0.025
T
GERP RS
-5.0
Varity_R
0.86
gMVP
0.99

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: rs28935490; hg19: chrX-100653420; COSMIC: COSV54510729; COSMIC: COSV54510729; API