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UGT1A1*6 AND Gilbert syndrome

Germline classification:
Conflicting interpretations of pathogenicity (6 submissions)
Last evaluated:
Apr 27, 2017
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000013071.54

Allele description [Variation Report for UGT1A1*6]

UGT1A1*6

Genes:
  • UGT1A:UDP glucuronosyltransferase family 1 member A complex locus [Gene - HGNC]
  • UGT1A10:UDP glucuronosyltransferase family 1 member A10 [Gene - OMIM - HGNC]
  • UGT1A1:UDP glucuronosyltransferase family 1 member A1 [Gene - OMIM - HGNC]
  • UGT1A3:UDP glucuronosyltransferase family 1 member A3 [Gene - OMIM - HGNC]
  • UGT1A4:UDP glucuronosyltransferase family 1 member A4 [Gene - OMIM - HGNC]
  • UGT1A5:UDP glucuronosyltransferase family 1 member A5 [Gene - OMIM - HGNC]
  • UGT1A6:UDP glucuronosyltransferase family 1 member A6 [Gene - OMIM - HGNC]
  • UGT1A7:UDP glucuronosyltransferase family 1 member A7 [Gene - OMIM - HGNC]
  • UGT1A8:UDP glucuronosyltransferase family 1 member A8 [Gene - OMIM - HGNC]
  • UGT1A9:UDP glucuronosyltransferase family 1 member A9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q37.1
Genomic location:
Preferred name:
UGT1A1*6
Other names:
NM_000463.2(UGT1A1):c.211G>A (p.Gly71Arg); 211G>A
HGVS:
  • NC_000002.12:g.233760498G>A
  • NG_002601.2:g.175755G>A
  • NG_033238.1:g.5226G>A
  • NM_000463.3:c.211G>AMANE SELECT
  • NM_001072.4:c.862-6536G>AMANE SELECT
  • NM_007120.3:c.868-6536G>AMANE SELECT
  • NM_019075.4:c.856-6536G>AMANE SELECT
  • NM_019076.5:c.856-6536G>AMANE SELECT
  • NM_019077.3:c.856-6536G>AMANE SELECT
  • NM_019078.2:c.868-6536G>AMANE SELECT
  • NM_019093.4:c.868-6536G>AMANE SELECT
  • NM_021027.3:c.856-6536G>AMANE SELECT
  • NM_205862.3:c.61-6536G>A
  • NP_000454.1:p.Gly71Arg
  • NP_000454.1:p.Gly71Arg
  • LRG_733t1:c.211G>A
  • LRG_733:g.5226G>A
  • LRG_733p1:p.Gly71Arg
  • NC_000002.11:g.234669144G>A
  • NM_000463.2:c.211G>A
Protein change:
G71R; Gly71Arg
Links:
Genetic Testing Registry (GTR): GTR000613302; Medical Genetics Summaries: UGT1A1*6; PharmGKB Clinical Annotation: 981201713; PharmGKB Clinical Annotation: 982047955; OMIM: 191740.0016; dbSNP: rs4148323
NCBI 1000 Genomes Browser:
rs4148323
Molecular consequence:
  • NM_001072.4:c.862-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007120.3:c.868-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_019075.4:c.856-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_019076.5:c.856-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_019077.3:c.856-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_019078.2:c.868-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_019093.4:c.868-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_021027.3:c.856-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_205862.3:c.61-6536G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000463.3:c.211G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
Decreased function

Condition(s)

Name:
Gilbert syndrome
Synonyms:
HYPERBILIRUBINEMIA I; HYPERBILIRUBINEMIA, ARIAS TYPE; Gilbert Disease; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007745; MedGen: C0017551; OMIM: 143500

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000033317OMIM
no assertion criteria provided
Affects
(Jan 1, 2013)
germlineliterature only

PubMed (8)
[See all records that cite these PMIDs]

SCV000249368Genetic Services Laboratory, University of Chicago
no assertion criteria provided
other
(Jan 25, 2016)
germlineclinical testing

SCV000428642Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Likely benign
(Apr 27, 2017)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV000538072Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 30, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001156253Difficult and Complicated Liver Diseases and Artificial Liver Center, Beijing You An Hospital, Capital Medical University
no assertion criteria provided
Pathogenic
(May 1, 2019)
inheritedcase-control

SCV005061255Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benigngermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
Chineseinheritedyes120not providednot providednot providednot providedcase-control

Citations

PubMed

A case of anorexia nervosa with hyperbilirubinaemia in a patient homozygous for a mutation in the bilirubin UDP-glucuronosyltransferase gene.

Maruo Y, Wada S, Yamamoto K, Sato H, Yamano T, Shimada M.

Eur J Pediatr. 1999 Jul;158(7):547-9.

PubMed [citation]
PMID:
10412811

Neonatal hyperbilirubinemia and mutation of the bilirubin uridine diphosphate-glucuronosyltransferase gene: a common missense mutation among Japanese, Koreans and Chinese.

Akaba K, Kimura T, Sasaki A, Tanabe S, Ikegami T, Hashimoto M, Umeda H, Yoshida H, Umetsu K, Chiba H, Yuasa I, Hayasaka K.

Biochem Mol Biol Int. 1998 Sep;46(1):21-6.

PubMed [citation]
PMID:
9784835
See all PubMed Citations (12)

Details of each submission

From OMIM, SCV000033317.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (8)

Description

This variant is designated UGT1A1*6 and rs4148323.

In a Japanese girl with anorexia nervosa and Gilbert syndrome (143500), Maruo et al. (1999) identified a homozygous 211G-A transition in exon 1 of the UGT1A1 gene, resulting in a gly71-to-arg substitution (G71R). The parents were heterozygous for the mutation.

Akaba et al. (1998) reported that the G71R mutation of the UGT1A1 gene, which in homozygous state causes Gilbert syndrome, is prevalent among Japanese, Korean, and Chinese populations, with a gene frequency of 0.13, 0.23, and 0.23, respectively. Akaba et al. (1999) showed that neonates carrying the G71R mutation have significantly increased bilirubin levels (237900) at days 2 to 4 in a gene dose-dependent manner and that the frequency of this mutation was significantly higher in the neonates who required phototherapy than in those who did not. They suggested that the G71R mutation contributes to the high incidence of neonatal hyperbilirubinemia in Japanese.

Among 20 children with acute leukemia, Kimura et al. (1999) found 4 with intermittent unconjugated hyperbilirubinemia during the course of combined chemotherapy. The G71R mutation was detected in the 4 patients with hyperbilirubinemia but was not found in the other 16 patients. Two of the 4 were heterozygotes; one was a homozygote for the G71R mutation; and the other was a compound heterozygote for G71R and the TA insertion mutation in the TATA box (191740.0011).

Maruo et al. (2000) analyzed 17 breastfed Japanese infants with apparent prolonged jaundice (serum bilirubin greater than 10 mg/dL at age 3 weeks to 1 month). When breastfeeding was stopped, the serum bilirubin levels began to decrease in all cases, but when breastfeeding was resumed, the serum bilirubin concentration again became elevated in some infants. Serum bilirubin levels normalized by the time the infants were 4 months old. Thus the infants had transient familial neonatal hyperbilirubinemia (237900). Sequencing of the UGT1A1 gene revealed that 8 infants were homozygous and 7 heterozygous for the G71R mutation. Another UGT1A1 missense mutation (191740.0017) was found in one of the G71R homozygotes, and an insertion in the TATA box of UGT1A1 (191740.0011) was found in one of the G71R heterozygotes.

Udomuksorn et al. (2007) found that the G71R mutant protein reduced the in vitro clearance for total bilirubin glucuronidation by 50% via a reduction in Vmax. The magnitude of decreases in clearance for other substrates varied according to substrate.

In a population-based study examining serum total bilirubin (BILIQTL1; 601816) in 3 Asian groups from Xinjiang, China, including 502 Kazakh herdsmen, 769 Uygur farmers, and 789 Han farmers, Lin et al. (2009) found a significant association with 2 polymorphisms in the UGT1A1 gene: the TA(n) repeat polymorphism (191740.0011) and rs4148323 (p = 2.05 x 10(-26) and p = 5.21 x 10(-16) respectively). The TA(7) allele and the A allele of rs4148323 were independently associated with increased total bilirubin levels. Combined, these SNPs could explain between 3.9 to 9.8% of the variance in these populations. The frequency of the A allele of rs4148323 for the Han, Uygur, and Kazakh populations was 0.211, 0.168, and 0.211, respectively, and could explain 9.8%, 4.5%, and 3.9%, respectively, of the total variation in bilirubin levels,

Sato et al. (2013) found that 56 (14%) of 401 Japanese neonates who were exclusively breastfed developed hyperbilirubinemia and required phototherapy. Neonates with a 10% or greater loss of body weight since birth had a significantly higher peak bilirubin level and incidence of hyperbilirubinemia, higher frequency of cesarean delivery, and shorter gestational period compared to those with less than 10% loss of body weight. Sex and body weight at birth were not significantly different between the 2 groups. UGT1A1 genotyping of the entire cohort showed that the frequency of the G71R polymorphism was 0.18 and was higher in neonates with body weight loss less than 10%. However, maximal body weight loss during the neonatal period was the only independent risk factor for the development of neonatal hyperbilirubinemia (odds ratio of 1.25). Although presence of the G71R variant was not a significant independent risk factor for neonatal hyperbilirubinemia overall, subgroup analysis revealed that G71R was a risk factor only in neonates with a 5% or greater maximal body weight loss, and the influence correlated with the degree of body weight loss. Sato et al. (2013) suggested that adequate feeding in the neonatal period may overcome the genetic predisposing factor of G71R to neonatal hyperbilirubinemia.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000249368.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000428642.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen, SCV000538072.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.211G>A (p.Gly71Arg) missense variant in the UGT1A1 gene is a known common variant associated with Gilbert Syndrome and hyperbilirubinemia in individuals of East Asian descent. Numerous case-control studies have demonstrated this variant is significantly prevalent in affected individuals relative to unaffected controls (Fu and Liu, 2005; Lin et al., 2009; Zhou et al., 2009; Prachukthum et al., 2009; Gao et al., 2010; Long et al., 2011a; Long et al., 2011b; Chen et al., 2014). Multiple in vitro studies have shown that this variant leads to reduced enzymatic activity, and this variant is associated with elevated serum bilirubin in infants (Yamamoto et al., 1998; Sneitz et al., 2010; Chou et al., 2011). The allele frequency is high in the population databases for individuals of East Asian descent, which is expected given the high prevalence of the disease (1000 Genomes = 13.8% [EAS]; ExAC = 15.24% [EAS]). Hence, a yet unknown genetic modifier that is specific to the East Asian population may contribute to the high disease prevalence. Finally, a reputable clinical diagnostic laboratory has reported this variant as Likely Pathogenic (University of Chicago). Together, this collective evidence supports the classification of the c.211G>A (p.Gly71Arg) as a Likely Pathogenic variant for Gilbert Syndrome.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From Difficult and Complicated Liver Diseases and Artificial Liver Center, Beijing You An Hospital, Capital Medical University, SCV001156253.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Chinese120not providednot providedcase-controlnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided120not providednot providednot provided

From Neuberg Centre For Genomic Medicine, NCGM, SCV005061255.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The missense variant c.211G>A (p.Gly71Arg) in the UGT1A1 gene has been reported previously in compound heterozygous and homozygous state in individuals affected with Gilbert's syndrome and Crigler-Najjar syndrome type II. Experimental studies have shown that this missense change affects UGT1A1 function (Gu et al., 2022; Sneitz et al., 2010; Yamamoto et al., 1998). This variant is reported with a high allele frequency in the gnomAD. It is submitted to ClinVar with varying interpretations as Pathogenic/ Likely Pathogenic/Uncertain significance/Likely benign/Benign. In a meta-analysis study, the result suggests that the p.Gly71Arg mutation of the UGT1A1 gene is a risk factor for developing neonatal hyperbilirubinemia in both Asians and Caucasian subjects (Mehrad-Majd et al., 2019). The amino acid Glycine at position 71 is changed to an Arginine changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted as damaging by SIFT. The amino acid change p.Gly71Arg in UGT1A1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Likely Benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 25, 2024