VCV002634101.1 - ClinVar

NM_000463.2(UGT1A1):c.-85_-83dupCAT

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000463.2(UGT1A1):c.-85_-83dupCAT

Variation ID: 2634101 Accession: VCV002634101.1

Type and length

Duplication, 3 bp

Location

Cytogenetic: 2q37.1 2: 233760202-233760203 (GRCh38) [ NCBI UCSC ] 2: 234668848-234668849 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 20, 2023	Nov 20, 2023	Jun 19, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001072.4:c.862-6831_862-6829dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_007120.3:c.868-6831_868-6829dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_019075.4:c.856-6831_856-6829dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_019076.5:c.856-6831_856-6829dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_019077.3:c.856-6831_856-6829dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_019078.2:c.868-6831_868-6829dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_019093.4:c.868-6831_868-6829dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_021027.3:c.856-6831_856-6829dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_205862.3:c.61-6831_61-6829dup		intron variant
NC_000002.12:g.233760203_233760205dup
NC_000002.11:g.234668849_234668851dup
NG_002601.2:g.175460_175462dup
NG_033238.1:g.4931_4933dup
LRG_733:g.4931_4933dup
LRG_733t1:c.-85_-83dup

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000002.12:233760202:CAT:CATCAT

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
UGT1A	-	-	-	GRCh38	-	587
UGT1A1		-	-	GRCh38 GRCh37	2	371
UGT1A10		-	-	GRCh38 GRCh37	-	589
UGT1A3		-	-	GRCh38 GRCh37	-	395
UGT1A4		-	-	GRCh38 GRCh37	-	421
UGT1A5		-	-	GRCh38 GRCh37	-	439
UGT1A6		-	-	GRCh38 GRCh37	-	482
UGT1A7		-	-	GRCh38 GRCh37	-	534
UGT1A8		-	-	GRCh38 GRCh37	-	617
UGT1A9		-	-	GRCh38 GRCh37	-	569

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
UGT1A1-related disorder	Pathogenic (1)	criteria provided, single submitter	Jun 19, 2023	RCV004531667.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Jun 19, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	UGT1A1-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004118134.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Comment: The UGT1A1 c.-85_-83dupCAT variant is located in the 5' untranslated region. This variant has been reported in the homozygous state, or in the heterozygous state … (more) The UGT1A1 c.-85_-83dupCAT variant is located in the 5' untranslated region. This variant has been reported in the homozygous state, or in the heterozygous state with a second UGT1A1 variant, in multiple patients with Gilbert syndrome and Crigler-Najjar syndrome type II (Farheen et al. 2006. PubMed ID: 16610035; van Dijk et al. 2015. PubMed ID: 26220753; Kumar et al. 2017. PubMed ID: 28892962; Shi et al. 2019. PubMed ID: 31142299). This variant is expected to interrupt the HNF1α binding site and impairs UGT1A1 promoter activity (van Dijk et al. 2015. PubMed ID: 26220753). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Taken together we interpret this variant as pathogenic. (less)

Comment:

The UGT1A1 c.-85_-83dupCAT variant is located in the 5' untranslated region. This variant has been reported in the homozygous state, or in the heterozygous state with a second UGT1A1 variant, in multiple patients with Gilbert syndrome and Crigler-Najjar syndrome type II (Farheen et al. 2006. PubMed ID: 16610035; van Dijk et al. 2015. PubMed ID: 26220753; Kumar et al. 2017. PubMed ID: 28892962; Shi et al. 2019. PubMed ID: 31142299). This variant is expected to interrupt the HNF1α binding site and impairs UGT1A1 promoter activity (van Dijk et al. 2015. PubMed ID: 26220753). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Taken together we interpret this variant as pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Oct 27, 2024

ClinVar Genomic variation as it relates to human health

NM_000463.2(UGT1A1):c.-85_-83dupCAT

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...