NM_000463.3(UGT1A1):c.1198A>G (p.Asn400Asp) AND UGT1A1-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 21, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV004528106.1

Allele description [Variation Report for NM_000463.3(UGT1A1):c.1198A>G (p.Asn400Asp)]

NM_000463.3(UGT1A1):c.1198A>G (p.Asn400Asp)

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:

NM_000463.3(UGT1A1):c.1198A>G (p.Asn400Asp)

HGVS:

NC_000002.12:g.233768333A>G
NG_002601.2:g.183590A>G
NG_033238.1:g.13061A>G
NM_000463.3:c.1198A>GMANE SELECT
NM_001072.4:c.1195A>GMANE SELECT
NM_007120.3:c.1201A>GMANE SELECT
NM_019075.4:c.1189A>GMANE SELECT
NM_019076.5:c.1189A>GMANE SELECT
NM_019077.3:c.1189A>GMANE SELECT
NM_019078.2:c.1201A>GMANE SELECT
NM_019093.4:c.1201A>GMANE SELECT
NM_021027.3:c.1189A>GMANE SELECT
NM_205862.3:c.394A>G
NP_000454.1:p.Asn400Asp
NP_000454.1:p.Asn400Asp
NP_001063.2:p.Asn399Asp
NP_001063.2:p.Asn399Asp
NP_009051.1:p.Asn401Asp
NP_009051.1:p.Asn401Asp
NP_061948.1:p.Asn397Asp
NP_061948.1:p.Asn397Asp
NP_061949.3:p.Asn397Asp
NP_061949.3:p.Asn397Asp
NP_061950.2:p.Asn397Asp
NP_061950.2:p.Asn397Asp
NP_061951.1:p.Asn401Asp
NP_061951.1:p.Asn401Asp
NP_061966.1:p.Asn401Asp
NP_061966.1:p.Asn401Asp
NP_066307.1:p.Asn397Asp
NP_066307.1:p.Asn397Asp
NP_995584.1:p.Asn132Asp
NP_995584.1:p.Asn132Asp
LRG_733t1:c.1198A>G
LRG_733:g.13061A>G
LRG_733p1:p.Asn400Asp
NC_000002.11:g.234676979A>G
NM_000463.2:c.1198A>G
NM_001072.3:c.1195A>G
NM_007120.2:c.1201A>G
NM_019075.2:c.1189A>G
NM_019076.4:c.1189A>G
NM_019077.2:c.1189A>G
NM_019078.1:c.1201A>G
NM_019093.2:c.1201A>G
NM_021027.2:c.1189A>G
NM_205862.1:c.394A>G
P22309:p.Asn400Asp

Protein change:

N132D; ASN400ASP

Links:

UniProtKB: P22309#VAR_019412; OMIM: 191740.0022; dbSNP: rs28934877

NCBI 1000 Genomes Browser:

rs28934877

Molecular consequence:

NM_000463.3:c.1198A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001072.4:c.1195A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_007120.3:c.1201A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_019075.4:c.1189A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_019076.5:c.1189A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_019077.3:c.1189A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_019078.2:c.1201A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_019093.4:c.1201A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_021027.3:c.1189A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_205862.3:c.394A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: UGT1A1-related disorder
Synonyms:: UGT1A1-Related Disorders; UGT1A1-related condition
Identifiers:

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Mus musculus nudix hydrolase 4 (Nudt4), transcript variant 2, mRNA
Mus musculus nudix hydrolase 4 (Nudt4), transcript variant 2, mRNA
gi|1313953526|ref|NM_027722.5|

Nucleotide
Xanthomonas oryzae pv. oryzae strain PX0124 scaffold357, whole genome shotgun se...
Xanthomonas oryzae pv. oryzae strain PX0124 scaffold357, whole genome shotgun sequence
gi|1426583149|ref|NZ_QNOE01000358.1 |WGS:NZ_QNOE01|scaffold357

Nucleotide
Xanthomonas oryzae pv. oryzae strain PX0124 scaffold292, whole genome shotgun se...
Xanthomonas oryzae pv. oryzae strain PX0124 scaffold292, whole genome shotgun sequence
gi|1426583084|ref|NZ_QNOE01000293.1 |WGS:NZ_QNOE01|scaffold292

Nucleotide
Listeria monocytogenes strain L1336 contig69, whole genome shotgun sequence
Listeria monocytogenes strain L1336 contig69, whole genome shotgun sequence
gi|2211909027|ref|NZ_JAGSFN01000004 gnl|WGS:NZ_JAGSFN01|contig69

Nucleotide
TPA_asm: Listeria monocytogenes strain DMG1500211 isolate Listeria monocytogenes...
TPA_asm: Listeria monocytogenes strain DMG1500211 isolate Listeria monocytogenes, whole genome shotgun sequencing project
gi|1772891439|tpg|DAAFBV000000000.1 BV010000000

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000915898	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 09 May 2019)	Uncertain significance (Nov 21, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24492252, 12402338 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000915898

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)

Uncertain significance
(Nov 21, 2018)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

PharmGKB summary: very important pharmacogene information for UGT1A1.

Barbarino JM, Haidar CE, Klein TE, Altman RB.

Pharmacogenet Genomics. 2014 Mar;24(3):177-83. doi: 10.1097/FPC.0000000000000024. Review. No abstract available.

PubMed [citation]

PMID:: 24492252
PMCID:: PMC4091838

Association of a homozygous (TA)8 promoter polymorphism and a N400D mutation of UGT1A1 in a child with Crigler-Najjar type II syndrome.

Labrune P, Myara A, Chalas J, Le Bihan B, Capel L, Francoual J.

Hum Mutat. 2002 Nov;20(5):399-401. No abstract available.

PubMed [citation]

PMID:: 12402338

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000915898.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The UGT1A1 c.1198A>G (p.Asn400Asp) missense variant has been reported in one study and is found in a total of three patients including one in a homozygous state with Crigler-Najjar syndrome type II (CN-II) and two in a heterozygous state with Gilbert syndrome (Labrune et al. 2002). The patient with CN-II carried a second homozygous variant in the TATA box promoter region identified as UGT1A1*37. The p.Asn400Asp variant was absent from 50 control chromosomes and is reported at a frequency of 0.00007 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the limited evidence, the p.Asn400Asp variant is classified as a variant of unknown significance but suspicious for pathogenicity for UGT1A1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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