rs111033640

Positions:

• chr9-34646575-CCAGT-C
• chr9-34646575-CCAGT-CCAGTCAGT

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP5 BA1

The ENST00000605275.1(GALT):​n.209-91_209-88del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0587 in 1,216,800 control chromosomes in the GnomAD database, including 2,445 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity,other (no stars).

• Frequency:
  • Genomes: 𝑓 0.047 (259 hom., cov: 31)
  • Exomes 𝑓: 0.060 (2186 hom.)
• Consequence: GALT ENST00000605275.1 intron, non_coding_transcript
• Clinical Significance: Conflicting classifications of pathogenicity; other criteria provided, conflicting classifications P:10 U:1 B:1 O:1
• Conservation: PhyloP100: 0.263

Genes affected

GALT (HGNC:4135): (galactose-1-phosphate uridylyltransferase) Galactose-1-phosphate uridyl transferase (GALT) catalyzes the second step of the Leloir pathway of galactose metabolism, namely the conversion of UDP-glucose + galactose-1-phosphate to glucose-1-phosphate + UDP-galactose. The absence of this enzyme results in classic galactosemia in humans and can be fatal in the newborn period if lactose is not removed from the diet. The pathophysiology of galactosemia has not been clearly defined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• PP5: Variant 9-34646575-CCAGT-C is Pathogenic according to our data. Variant chr9-34646575-CCAGT-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity, other]. Clinvar id is 25111.We mark this variant Likely_pathogenic, oryginal submissions are: {other=1, Likely_pathogenic=2, Uncertain_significance=1, Pathogenic=7}.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALT	ENST00000605275.1	n.209-91_209-88del		intron_variant, non_coding_transcript_variant		3
GALT	ENST00000450095.6			upstream_gene_variant		2		ENSP00000401956

Frequencies

GnomAD3 genomes AF: 0.0471 AC: 7161 AN: 152148 Hom.: 258 Cov.: 31

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0490

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.00943

Gnomad SAS AF: 0.0690

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0440

GnomAD4 exome AF: 0.0603 AC: 64222 AN: 1064534 Hom.: 2186 AF XY: 0.0610 AC XY: 33204 AN XY: 544444

Gnomad4 AFR exome AF: 0.0111

Gnomad4 AMR exome AF: 0.0491

Gnomad4 ASJ exome AF: 0.0510

Gnomad4 EAS exome AF: 0.00640

Gnomad4 SAS exome AF: 0.0758

Gnomad4 FIN exome AF: 0.0679

Gnomad4 NFE exome AF: 0.0636

Gnomad4 OTH exome AF: 0.0570

GnomAD4 genome AF: 0.0470 AC: 7163 AN: 152266 Hom.: 259 Cov.: 31 AF XY: 0.0468 AC XY: 3488 AN XY: 74466

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0491

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.00926

Gnomad4 SAS AF: 0.0689

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0553 Hom.: 30

Bravo AF: 0.0422

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity; other

Submissions summary: Pathogenic:10 Uncertain:1 Benign:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Pathogenic:5 Benign:1

Benign, no assertion criteria provided	literature only	GeneReviews	Sep 23, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jun 03, 2022	The GALT c.-119_-116delGTCA variant (rs1275569312) is commonly found as part of the Duarte (D2) allele that is associated with mild decreases of GALT activity compared to the wildtype allele (Andersen 1984, Elsas 1994, Kozak 1999. Lai 1998, Langley 1997, Shin 1998). Functional characterization of the complex variant indicates a reduction in mRNA transcription due to the deletion in the promoter region (Elsas 2001, Trbusek 2001). Based on the above information, the variant is classified as mildly pathogenic. References: Andersen M et al. Transferase-deficiency galactosemia: immunochemical studies of the Duarte and Los Angeles variants. Hum Genet. 1984; 65(3):287-90. Elsas LJ et al. A common mutation associated with the Duarte galactosemia allele. Am J Hum Genet. 1994; 54(6):1030-6. Elsas LJ et al. Functional analysis of the human galactose-1-phosphate uridyltransferase promoter in Duarte and LA variant galactosemia. Genet Metab. 2001; 72(4):297-305. Kozak L et al. Presence of a deletion in the 5' upstream region of the GALT gene in Duarte (D2) alleles. J Med Genet. 1999; 36(7):576-8. Lai K et al. Duarte allele impairs biostability of galactose-1-phosphate uridyltransferase in human lymphoblasts.Hum Mutat. 1998; 11(1):28-38. Langley S et al. Molecular basis for Duarte and Los Angeles variant galactosemia. Am J Hum Genet. 1997; 60(2):366-72. Shin Y et al. Duarte-1 (Los Angeles) and Duarte-2 (Duarte) variants in Germany: two new mutations in the GALT gene which cause a GALT activity decrease by 40-50% of normal in red cells. J Inherit Metab Dis. 1998; 21(3):232-5. Trbusek M et al. Galactosemia: deletion in the 5' upstream region of the GALT gene reduces promoter efficiency. Hum Genet. 2001; 109(1):117-20. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Pars Genome Lab	May 18, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Breda Genetics srl	Nov 09, 2021	The Duarte variant galactosemia is diagnosed in the presence of one heterozygous pathogenic GALT variant together with either a heterozygous or homozygous Duarte (D2) GALT variant. Five sequence changes in cis configuration are found on the Duarte variant (D2) allele. Of primary importance is the 4-bp deletion in the GALT promoter region (c.-119_-116delGTCA) that is considered to cause diminished transcription. The three remaining variants unique to D2 are c.378-27G>C, c.508-24G>A, and c.507+62G>A. The fifth sequence change is the missense variant c.940A>G (p.Asn314Asp); while always on the D2 allele, c.940A>G also occurs on other functionally normal GALT alleles (Fridovich-Keil et al., 2020, PMID: 25473725). -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 12, 2021	This variant occurs in a non-coding region of the GALT gene. It does not change the encoded amino acid sequence of the GALT protein. This variant is present in population databases (rs142496102, gnomAD 8%), including at least one homozygous and/or hemizygous individual. This variant is unique to the D2 allele and is a well-known cause of Duarte galactosemia with a partial reduction, typically 14%-25% of wild-type GALT enzyme activity (PMID: 25473725). ClinVar contains an entry for this variant (Variation ID: 25111). 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 GALT function (PMID: 11286503, 11479743, 19224951). For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -

not provided Pathogenic:3 Other:1

other, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 23, 2018	- Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles).
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2024	GALT: PM3:Very Strong, PM2:Supporting, PP4, PS3:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 28, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 28, 2022	The c.-119_-116delGTCA promoter variant (Duarte 2 variant) causes a reduction in GALT transcription resulting in approximately 50% of normal galactose-1-phosphate uridyltransferase (GALT) activity in individuals who are homozygous for this allele (Langley et al., 1997; Bosch et al., 2005; Carney et al., 2009); Common variant observed in 8% (278/3470) of alleles from individuals of European background (gnomAD); This variant is associated with the following publications: (PMID: 10424825, 11286503, 11479743, 19224951, 15841485, 10649501, 11754113, 25473725, 34030713) -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 15, 2023

The c.-119_-116delGTCA alteration is located in the 5' untranslated region (5'UTR) of the GALT gene. This alteration consists of a deletion of 4 nucleotides upstream from the first translated codon. ; however, this variant is known as the Duarte (D2) allele and is considered a mild allele associated with a biochemical phenotype. Based on data from gnomAD, the c.-119_-116delGTCA allele has an overall frequency of 4.889% (1533/31354) total alleles studied. The highest observed frequency was 8.012% (278/3470) of European (Finnish) alleles. This alteration is more common in population databases than expected for likely pathogenic/disease-causing variants (Pyhtila, 2015). This alteration is unique to the Duarte (D2) allele and is a cause of Duarte galactosemia, associated with a mild to asymptomatic phenotype. This alteration has been reported in asymptomatic individuals identified by newborn screening (Carney, 2009; Garcia, 2016). This nucleotide position is well conserved in available vertebrate species. Functional studies have shown that this deletion decreases GALT mRNA production and enzyme activity (Kozák, 1999; Elsas, 2001; Trbusek, 2001; Carney, 2009). In silico analysis was unable to predict the effect of this alteration. Based on the available evidence, this alteration is classified as pathogenic. -

Classical galactosemia, homozygous Duarte-type Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

May 01, 2009

- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Jun 15, 2022

Variant summary: GALT c.-119_-116delGTCA involves the deletion of a stretch of four nucleotides located in the GALT promoter region. The variant allele was found at a frequency of 0.046 in 150922 control chromosomes in the gnomAD database, including 242 homozygotes (gnomAD v3.1.2). Even though this frequency exceeds the maximal expected allele frequency for a pathogenic variant in GALT (0.0029), this variant is found in cis with 4 other (benign) variants as part of the Duarte 2 variant (D2) allele and it has been reported in the literature in multiple individuals with a biochemical diagnosis of Duarte galactosemia (DG) (e.g. Elsas_2001, Yang_2002). This form of galactosemia is caused by the presence of one heterozygous pathogenic GALT variant together with either a heterozygous or homozygous Duarte GALT variant, resulting in a reduction of GALT enzyme activity that is typically about 25% of normal activity (Pasquali_2018, Fridovich-Keil_2020). Experimental evidence evaluating an impact on protein function demonstrated c.-119_-116delGTCA to reduce promoter activity, causing diminished transcription of the gene eventually resulting in reduced GALT activity (Elsas_2001, Trbusek_2001, Carney_2009). The variant causes a milder effect on the enzyme activity than classic GALT pathogenic variants (carriers of the variant show about 75% of wild-type activity) (Elsas_2001). However, more recent publications put into question the clinical relevance of the D2 variant. Specifically, international clinical guidelines released by The Galactosemia Network (GalNet) recommend to not treat patients with the Duarte variant and to not provide endocrine follow-up, as there is no evidence that the ovaries are affected (Welling_2017). The authors review evidence from the literature reporting long-term outcomes in DG indicative of normal IQ scores, language skills, FSH values, and ophthalmologic examinations in untreated DG children aged 1-6 years (PMIDs: 18976948, 20489133) and comparable levels of FSH in female children with DG (up to 10.5 years) vs. healthy controls (PMID: 21719007). Nevertheless, Powell et al (PMID: 19904210) reported a higher percentage of children with DG enrolled in special education services compared to the general population, while a small pilot study identified some differences in socio-emotional development, in delayed recall, and in auditory processing speed between children with DG and their unaffected siblings (PMID: 25681083). Carlock et al (2019) and Fridovich-Keil et al (2021) conducted studies of dietary and developmental outcomes in children with DG (up to 12 years), and found no evidence of increased risk for acute complications or childhood developmental challenges that require intervention, regardless of milk exposure in infancy. Another study examined developmental outcomes and the need for special services in individuals with DG and concluded that Duarte-2 galactosemia may increase the risk for mild developmental delays during early infancy, but these are transient and dissipate with time (Waisbren_2021). Fridovich-Keil et al (2021) suggest based on their observations, that parents of infants diagnosed and treated for DG may be more motivated to seek special education services, which may explain the higher prevalence of this phenomenon in treated DG cases compared to their untreated DG counterparts. Seven ClinVar submitters (evaluation after 2014) cite the variant as pathogenic/likely pathogenic, while one ClinVar submitter cites it as other. In conclusion, based on the evidence outlined above, and in particular the emergence of new evidence indicative of normal long-term outcomes for individuals with Duarte galactosemia, the variant was re-classified as uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs111033640; hg19: chr9-34646572;