rs111033640
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP5BA1
The ENST00000605275.1(GALT):​n.209-101_209-98delCAGT variant causes a intron 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
Consequence
ENST00000605275.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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Ensembl
Frequencies
GnomAD3 genomes 0.0471 AC: 7161AN: 152148Hom.: 258 Cov.: 31
GnomAD4 exome AF: 0.0603 AC: 64222AN: 1064534Hom.: 2186 AF XY: 0.0610 AC XY: 33204AN XY: 544444
GnomAD4 genome 0.0470 AC: 7163AN: 152266Hom.: 259 Cov.: 31 AF XY: 0.0468 AC XY: 3488AN XY: 74466
ClinVar
Submissions by phenotype
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Pathogenic:5Benign:1
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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. -
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). -
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. -
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not provided Pathogenic:3Other:1
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) -
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- Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles).
GALT: PM3:Very Strong, PM2:Supporting, PP4, PS3:Supporting -
Inborn genetic diseases Pathogenic:1
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. -
Galactosemia Pathogenic:1
PS3,PM3(strong),PM2,PP4 -
Classical galactosemia, homozygous Duarte-type Pathogenic:1
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not specified Uncertain:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at