chr2-69326167-G-T

Position:

• chr2-69326167-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP5 BS2

The NM_001244710.2(GFPT1):​c.*22C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00197 in 1,511,390 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0020 (5 hom.)
• Consequence: GFPT1 NM_001244710.2 3_prime_UTR
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:8 U:3
• Conservation: PhyloP100: 0.525

Genes affected

GFPT1 (HGNC:4241): (glutamine--fructose-6-phosphate transaminase 1) This gene encodes the first and rate-limiting enzyme of the hexosamine pathway and controls the flux of glucose into the hexosamine pathway. The product of this gene catalyzes the formation of glucosamine 6-phosphate. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PP5: Variant 2-69326167-G-T is Pathogenic according to our data. Variant chr2-69326167-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 208585.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=4, Pathogenic=2, Uncertain_significance=3}. Variant chr2-69326167-G-T is described in Lovd as [Pathogenic].
• BS2: High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GFPT1	NM_001244710.2	c.*22C>A		3_prime_UTR_variant	20/20	ENST00000357308.9	NP_001231639.1
GFPT1	NM_002056.4	c.*22C>A		3_prime_UTR_variant	19/19		NP_002047.2
GFPT1	XM_017003801.2	c.*22C>A		3_prime_UTR_variant	20/20		XP_016859290.1
GFPT1	XM_017003802.3	c.*22C>A		3_prime_UTR_variant	19/19		XP_016859291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GFPT1	ENST00000357308.9	c.*22C>A		3_prime_UTR_variant	20/20	5	NM_001244710.2	ENSP00000349860
GFPT1	ENST00000361060.5	c.*22C>A		3_prime_UTR_variant	19/19	1		ENSP00000354347	P1
GFPT1	ENST00000674438.1	c.*22C>A		3_prime_UTR_variant	17/17			ENSP00000501469
GFPT1	ENST00000674507.1	c.*22C>A		3_prime_UTR_variant	18/18			ENSP00000501332

Frequencies

GnomAD3 genomes AF: 0.00143 AC: 216 AN: 151010 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000414

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00245

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000293

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00228

Gnomad OTH AF: 0.00145

GnomAD3 exomes AF: 0.00133 AC: 333 AN: 249944 Hom.: 0 AF XY: 0.00138 AC XY: 186 AN XY: 135082

Gnomad AFR exome AF: 0.000433

Gnomad AMR exome AF: 0.000987

Gnomad ASJ exome AF: 0.000199

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000330

Gnomad NFE exome AF: 0.00241

Gnomad OTH exome AF: 0.00164

GnomAD4 exome AF: 0.00203 AC: 2761 AN: 1360264 Hom.: 5 Cov.: 22 AF XY: 0.00193 AC XY: 1315 AN XY: 682390

Gnomad4 AFR exome AF: 0.000414

Gnomad4 AMR exome AF: 0.00117

Gnomad4 ASJ exome AF: 0.0000786

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000119

Gnomad4 FIN exome AF: 0.000323

Gnomad4 NFE exome AF: 0.00251

Gnomad4 OTH exome AF: 0.00199

GnomAD4 genome AF: 0.00142 AC: 215 AN: 151126 Hom.: 0 Cov.: 32 AF XY: 0.00138 AC XY: 102 AN XY: 73708

Gnomad4 AFR AF: 0.000413

Gnomad4 AMR AF: 0.00244

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000293

Gnomad4 NFE AF: 0.00227

Gnomad4 OTH AF: 0.00144

Alfa AF: 0.000502 Hom.: 0

Bravo AF: 0.00165

Asia WGS AF: 0.000289 AC: 1 AN: 3476

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:8 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:4 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	GFPT1: PM3:Strong, PP1:Strong, PM2:Supporting, PS3:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Mar 31, 2017	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 24, 2024	Published functional studies suggest a damaging effect with the formation of a microRNA binding site resulting in reduced protein expression (PMID: 25765662); This variant is associated with the following publications: (PMID: 21310273, 26501342, 23488891, 27472506, 21975507, 26721333, 28754144, 29054425, 31047772, 23794683, 34978387, 36188410, 25765662, 28712002, 37721175, 38235042) -

Congenital myasthenic syndrome 12 Pathogenic:3 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Feb 25, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Apr 12, 2020	This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Sep 21, 2018	The GFPT1 c.*22C>A variant has been reported in at least three studies in which it is found in a compound heterozygous state in eight unrelated probands from a total of 13 affected individuals, and in a heterozygous state in four asymptomatic relatives (Senderek et al. 2011; Maselli et al. 2013; Selcen et al. 2013). The c.*22C>A variant was absent from 635 control subjects (Senderek et al. 2011) and is reported at a frequency of 0.002462 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies in myoblast cell lines derived from patients carrying the c.*22C>A variant showed reduction in GFPT1 protein levels, while the level of mRNA was similar to wild type GFPT1 (Dusl et al. 2015). In silico analysis and an in vitro reporter gene assay indicated that the c.*22C>A variant leads to a gain of putative binding sites for a microRNA, which was shown to mediate the reduction in GFPT1 protein expression (Dusl et al. 2015). Despite the available clinical data, the frequency of the variant in the public databases is too high to be causative of disease based on the known disease prevalence and penetrance. Therefore taking into account the conflicting evidence, the c.*22C>A variant is classified as a variant of unknown significance but suspicious for pathogenicity for the autosomal recessive form of congenital myasthenic syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	This variant occurs in a non-coding region of the GFPT1 gene. It does not change the encoded amino acid sequence of the GFPT1 protein. This variant is present in population databases (rs199678034, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individual(s) with congenital myasthenic syndrome (PMID: 21310273, 23488891, 23794683). 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: 208585). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects GFPT1 function (PMID: 21310273, 25765662). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic. -

Congenital myasthenic syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Sep 04, 2024

Variant summary: GFPT1 c.*22C>A is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 0.002 in 1504712 control chromosomes, predominantly at a frequency of 0.0025 within the Non-Finnish European subpopulation in the gnomAD database, including 5 homozygotes. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 5 fold of the estimated maximal expected allele frequency for a pathogenic variant in GFPT1 causing Congenital Myasthenic Syndrome (CMS) phenotype (0.0005). The observed relatively high frequency in non-Finnish Europeans, together with the homozygous occurrences, might indicate a benign nature for the variant. However, the variant c.*22C>A has also been reported in the literature in numerous compound heterozygous individuals, who were affected with Congenital Myasthenic Syndrome, including multiple cases where the variant segregated with disease (e.g. Senderek_2011, Selcen_2013, Maselli_2014, Natera-de Benito_2017, Bauche_2017). These data indicate that the variant is likely to be associated with disease, although the pathogenicity of the variant might be dependent on the variant observed in trans. At least two publications report that GFPT1 protein, but not mRNA levels, are reduced in muscle cells from patients harboring the c.*22C>A variant compared to healthy control individuals (e.g. Senderek_2011, Dusl_2015) and a similar relationship was observed in myoblasts expressing the variant compared to wild-type (Dusl_2015). One of these publications also provided evidence to support that the variant may allow for binding of a microRNA, that is expressed in myoblasts, myotubes and skeletal muscle, which may cause the reduction in GFPT1 protein expression by repressing translation (Dusl_2015). The following publications have been ascertained in the context of this evaluation (PMID: 25765662, 23488891, 23794683, 21310273, 29054425, 28712002). ClinVar contains an entry for this variant (Variation ID: 208585). Based on the evidence outlined above, the variant likely represents a hypomorphic allele, which in compound heterozygous state, together with other (likely more severe) variants in trans, can cause CMS and related phenotypes, therefore, the variant was classified as likely pathogenic. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Feb 27, 2019

Variant classified as Uncertain Significance - Favor Pathogenic. The c.*22C>A variant in GFPT1 has been reported in 8 individuals with features of limb-girdle myasthenic syndrome (Senderek 2011, Selcen 2013, Bauche 2017, Natera-de Benito 2017). All of these individuals carried second variants in the GFPT1 gene; however, in only 3 of these probands were the variants confirmed to be in trans and have sufficient evidence to be classified as likely pathogenic or pathogenic(Senderek 2011, Selcen 2013). Furthermore, the variant segregated with disease in 7 affected individuals from 5 families (Senderek 2011, Selcen 2013). It has also been identified in 0.23% (297/128550) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org), and has been reported with conflicting interpretations in ClinVar (Variant ID 208585). This variant is located in the 3' untranslated region. In vitro functional studies provide some evidence that the c.*22C>A variant may lead to reduced GFPT1 protein levels by influencing miRNA binding and thereby protein translation (Senderek 2011, Muller 2012, Dusl 2015). However, the assay may not accurately represent the in vivo environment and the reduction in protein levels may not be sufficient for disease. While the biallelic occurrences, segregation in affected individuals, and in vitro functional studies support a disease-causing role, given the relatively high frequency of this variant in the general population, there is some concern that the biallelic occurrences may have been seen by chance (therefore the PM3 evidence was downgraded) or that the variant may be in linkage disequilibrium with another pathogenic variant in the families described (therefore PP1 evidence was downgraded). In summary, while there is some suspicion for a pathogenic role, the clinical significance of the c.*22C>A variant is uncertain. ACMG/AMP guidelines applied: BS1_Supporting, PM3_Supporting, PP1_Moderate, PS3_Supporting. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.59		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.59		Position offset: 4

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs199678034; hg19: chr2-69553299;