rs35350960

chr2-233760973-C-Achr2-233760973-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM5 BP4_Strong BS1_Supporting BS2

The NM_000463.3(UGT1A1):c.686C>A(p.Pro229Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000476 in 1,614,172 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity,other (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P229L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00083 (3 hom., cov: 33)
  • Exomes 𝑓: 0.00044 (12 hom.)
• Consequence: UGT1A1 NM_000463.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity; other criteria provided, conflicting classifications P:4 U:3 B:1 O:2
• Conservation: PhyloP100: 0.857

Genes affected

UGT1A1 (HGNC:12530): (UDP glucuronosyltransferase family 1 member A1) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The preferred substrate of this enzyme is bilirubin, although it also has moderate activity with simple phenols, flavones, and C18 steroids. Mutations in this gene result in Crigler-Najjar syndromes types I and II and in Gilbert syndrome. [provided by RefSeq, Jul 2008]

UGT1A6 (HGNC:12538): (UDP glucuronosyltransferase family 1 member A6) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene is active on phenolic and planar compounds. Alternative splicing in the unique 5' end of this gene results in two transcript variants. [provided by RefSeq, Jul 2008]

UGT1A4 (HGNC:12536): (UDP glucuronosyltransferase family 1 member A4) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. This enzyme has some glucuronidase activity towards bilirubin, although is is more active on amines, steroids, and sapogenins. [provided by RefSeq, Jul 2008]

UGT1A10 (HGNC:12531): (UDP glucuronosyltransferase family 1 member A10) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene has glucuronidase activity on mycophenolic acid, coumarins, and quinolines. [provided by RefSeq, Jul 2008]

UGT1A8 (HGNC:12540): (UDP glucuronosyltransferase family 1 member A8) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene has glucuronidase activity with many substrates including coumarins, phenols, anthraquinones, flavones, and some opioids. [provided by RefSeq, Jul 2008]

UGT1A7 (HGNC:12539): (UDP glucuronosyltransferase family 1 member A7) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene has moderate glucuronidase activity with phenols. [provided by RefSeq, Jul 2008]

UGT1A5 (HGNC:12537): (UDP glucuronosyltransferase family 1 member A5) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. [provided by RefSeq, Jul 2008]

UGT1A3 (HGNC:12535): (UDP glucuronosyltransferase family 1 member A3) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. Substrates of this enzyme include estrone, 2-hydroxyestrone, and metabolites of benzo alpha-pyrene. [provided by RefSeq, Jul 2008]

UGT1A9 (HGNC:12541): (UDP glucuronosyltransferase family 1 member A9) This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The locus includes thirteen unique alternate first exons followed by four common exons. Four of the alternate first exons are considered pseudogenes. Each of the remaining nine 5' exons may be spliced to the four common exons, resulting in nine proteins with different N-termini and identical C-termini. Each first exon encodes the substrate binding site, and is regulated by its own promoter. The enzyme encoded by this gene is active on phenols. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• PM5: Other missense variant is known to change same aminoacid residue: Variant chr2-233760973-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1409267.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Likely_pathogenic=1}.
• BP4: Computational evidence support a benign effect (MetaRNN=0.008823067).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000834 (127/152280) while in subpopulation EAS AF= 0.0181 (94/5180). AF 95% confidence interval is 0.0152. There are 3 homozygotes in gnomad4. There are 44 alleles in male gnomad4 subpopulation. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAd at 3 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGT1A1	NM_000463.3	c.686C>A	p.Pro229Gln	missense_variant	1/5	ENST00000305208.10
UGT1A6	NM_001072.4	c.862-6061C>A		intron_variant		ENST00000305139.11
UGT1A4	NM_007120.3	c.868-6061C>A		intron_variant		ENST00000373409.8
UGT1A10	NM_019075.4	c.856-6061C>A		intron_variant		ENST00000344644.10
UGT1A8	NM_019076.5	c.856-6061C>A		intron_variant		ENST00000373450.5
UGT1A7	NM_019077.3	c.856-6061C>A		intron_variant		ENST00000373426.4
UGT1A5	NM_019078.2	c.868-6061C>A		intron_variant		ENST00000373414.4
UGT1A3	NM_019093.4	c.868-6061C>A		intron_variant		ENST00000482026.6
UGT1A9	NM_021027.3	c.856-6061C>A		intron_variant		ENST00000354728.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT1A1	ENST00000305208.10	c.686C>A	p.Pro229Gln	missense_variant	1/5	1	NM_000463.3	P1
UGT1A6	ENST00000305139.11	c.862-6061C>A		intron_variant		1	NM_001072.4	P1
UGT1A10	ENST00000344644.10	c.856-6061C>A		intron_variant		1	NM_019075.4	P1
UGT1A9	ENST00000354728.5	c.856-6061C>A		intron_variant		1	NM_021027.3	P1
UGT1A4	ENST00000373409.8	c.868-6061C>A		intron_variant		1	NM_007120.3	P1
UGT1A5	ENST00000373414.4	c.868-6061C>A		intron_variant		1	NM_019078.2	P1
UGT1A7	ENST00000373426.4	c.856-6061C>A		intron_variant		1	NM_019077.3	P1
UGT1A8	ENST00000373450.5	c.856-6061C>A		intron_variant		1	NM_019076.5	P1
UGT1A3	ENST00000482026.6	c.868-6061C>A		intron_variant		1	NM_019093.4	P1

Frequencies

GnomAD3 genomes AF: 0.000828 AC: 126 AN: 152164 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00183

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.000956

GnomAD3 exomes AF: 0.00148 AC: 372 AN: 251388 Hom.: 3 AF XY: 0.00143 AC XY: 194 AN XY: 135886

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.0000867

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0193

Gnomad SAS exome AF: 0.000294

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.000439 AC: 642 AN: 1461892 Hom.: 12 Cov.: 34 AF XY: 0.000468 AC XY: 340 AN XY: 727246

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000894

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0119

Gnomad4 SAS exome AF: 0.000255

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000540

Gnomad4 OTH exome AF: 0.00227

GnomAD4 genome AF: 0.000834 AC: 127 AN: 152280 Hom.: 3 Cov.: 33 AF XY: 0.000591 AC XY: 44 AN XY: 74472

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00183

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0181

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.000946

Alfa AF: 0.000911 Hom.: 5

Bravo AF: 0.000937

ExAC AF: 0.00137 AC: 166

Asia WGS AF: 0.00895 AC: 31 AN: 3478

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity; other

Submissions summary: Pathogenic:4 Uncertain:3 Benign:1 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Uncertain:1 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Jan 18, 2024	This sequence change replaces proline, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 229 of the UGT1A1 protein (p.Pro229Gln). This variant is present in population databases (rs35350960, gnomAD 2.0%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individual(s) with Gilbert disease (PMID: 7715297, 8528206, 14616765). This variant is frequently observed to be in cis with the c.-41_-40dup (aka UGT1A1*28 or (TA)7) variant (PMID: 11316168, 19325249, 15304120) This variant is also known as UGT1A1*27. ClinVar contains an entry for this variant (Variation ID: 12274). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt UGT1A1 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects UGT1A1 function (PMID: 8528206, 18004206). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 26, 2023	The UGT1A1 c.686C>A, p.Pro229Gln variant (rs35350960; ClinVar Variation ID: 12274), also known as the UGT1A1*27 allele (Mackenzie 1997), is reported in the literature in individuals of East Asian descent affected with Gilbert syndrome, almost always with one or two copies of the pathogenic-mild UGT1A1 *28 promoter variant (Huang 2000, Koiwai 1995, Maruo 2003, Sai 2004, Sun 2017). Functional analyses of the p.Pro229Gln variant protein showed markedly reduced enzyme activity (Koiwai 1995, Udomuksorn 2007). Individuals heterozygous for the UGT1A1*27 allele may also be at increased risk for drug toxicity when treated with irinotecan (Ando 2000, Teh 2012). This variant is found predominantly in the East Asian population with an overall allele frequency of 1.9% (389/19954 alleles, including three homozygotes) in the Genome Aggregation Database. The proline at codon 229 is highly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.32). Based on available information, this variant is considered to be mildly pathogenic for Gilbert syndrome with reduced penetrance. References: Ando Y et al. Polymorphisms of UDP-glucuronosyltransferase gene and irinotecan toxicity: a pharmacogenetic analysis. Cancer Res. 2000 60:6921-6926. PMID: 11156391 Huang CS et al. Variations of the bilirubin uridine-diphosphoglucuronosyl transferase 1A1 gene in healthy Taiwanese. Pharmacogenetics. 2000 10:539-544. PMID: 10975608 Kaniwa N et al. Racial variability in haplotype frequencies of UGT1A1 and glucuronidation activity of a novel single nucleotide polymorphism 686C> T (P229L) found in an African-American. Drug Metab Dispos. 2005 33:458-465. PMID: 15572581 Koiwai O et al. Gilbert's syndrome is caused by a heterozygous missense mutation in the gene for bilirubin UDP-glucuronosyltransferase. Hum Mol Genet. 1995 4:1183-1186. PMID: 8528206 Mackenzie PI et al. The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence. Pharmacogenetics. 1997 7:255-269. PMID: 9295054 Maruo Y et al. Co-occurrence of three different mutations in the bilirubin UDP-glucuronosyltransferase gene in a Chinese family with Crigler-Najjar syndrome type I and Gilbert's syndrome. Clin Genet. 2003 64:420-423. PMID: 14616765 Sai K et al. UGT1A1 haplotypes associated with reduced glucuronidation and increased serum bilirubin in irinotecan-administered Japanese patients with cancer. Clin Pharmacol Ther. 2004 75:501-515. PMID: 15179405 Sun L et al. Differences in UGT1A1 gene mutations and pathological liver changes between Chinese patients with Gilbert syndrome and Crigler-Najjar syndrome type II. Medicine (Baltimore). 2017 96:e8620. PMID: 29137095 Teh LK et al. Polymorphisms of UGT1A1*6, UGT1A1*27 & UGT1A1*28 in three major ethnic groups from Malaysia. Indian J Med Res. 2012 136:249-259. PMID: 22960892 Udomuksorn W et al. Influence of mutations associated with Gilbert and Crigler-Najjar type II syndromes on the glucuronidation kinetics of bilirubin and other UDP-glucuronosyltransferase 1A substrates. Pharmacogenet Genomics. 2007 17:1017-1029. PMID: 18004206 -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jul 09, 2020	- -
other, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Sep 17, 2018	- Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles).

Gilbert syndrome Pathogenic:1 Other:1

Affects, no assertion criteria provided	literature only	OMIM	Dec 01, 2007	- -
Pathogenic, no assertion criteria provided	case-control	Difficult and Complicated Liver Diseases and Artificial Liver Center, Beijing You An Hospital, Capital Medical University	May 01, 2019	- -

not specified Uncertain:1 Benign:1

Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 19, 2020	The p.Pro229Gln variant in UGT1A1 has been reported in the heterogygous and compound heterozygous state in numerous individuals with Gilbert syndrome or Crigler-Najjar syndrome type II , however, most of them were also homozygous for other pathogenic variants in the gene. This variant has also been reported in ClinVar (Variation ID 12274). It has been identified in 1.9% (389/19954) of East Asian chromosomes by gnomAD (https://gnomad.broadinstitute.org/). Computational prediction tools and conservation analysis suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In vitro functional studies provide some evidence that this variant impacts protein function (Gagne 2002 PMID: 12181437, Udomuksorn 2007 PMID: 18004206); however, these types of assays may not accurately represent biological function. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PS3_Supporting, BS1_Supporting, BP4. -

Crigler-Najjar syndrome, type II Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Dec 01, 2007

- -

UGT1A1-related condition Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 08, 2024

The UGT1A1 c.686C>A variant is predicted to result in the amino acid substitution p.Pro229Gln. The minor allele frequency of this variant is over 1% in the East Asian sub-population, including 3 homozygotes, indicating this variant may be too common to be a primary cause of a Mendelian disease. However, an in vitro study indicated this variant caused a reduction in the activity of bilirubin UDP-glucuronosyltransferase (UGT) (Koiwai et al. 1995. PubMed ID: 8528206). The contribution of this variant to disease remains under debate (Kaniwa et al. 2005. PubMed ID: 15572581; Zhang et al. 2007. PubMed ID: 17060921; Wisnumurti et al. 2018. PubMed ID: 29607327), and classifications for this variant from outside laboratories range from benign to pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/12274/). Therefore, we classify c.686C>A (p.Pro229Gln) as a variant of uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.16
Cadd	Benign	14
Dann	Benign	0.97
DEOGEN2	Benign	0.23	T;.
Eigen	Benign	-0.39
Eigen_PC	Benign	-0.45
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.63	T;T
MetaRNN	Benign	0.0088	T;T
MetaSVM	Benign	-0.80	T
MutationAssessor	Uncertain	2.2	M;M
MutationTaster	Benign	0.68	N;N;N;N;N;N;N;N;N;N;N;N;N
PROVEAN	Benign	-2.1	N;D
REVEL	Uncertain	0.32
Sift	Benign	0.16	T;T
Sift4G	Benign	0.53	T;T
Polyphen		0.60	P;.
Vest4		0.34
MVP		0.62
MPC		0.45
ClinPred		0.11	T
GERP RS		4.9
Varity_R		0.12
gMVP		0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs35350960; hg19: chr2-234669619; COSMIC: COSV59386733; COSMIC: COSV59386733;