VCV003066040.1 - ClinVar

NM_000463.3(UGT1A1):c.1216_1225del (p.Thr406fs)

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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000463.3(UGT1A1):c.1216_1225del (p.Thr406fs)

Variation ID: 3066040 Accession: VCV003066040.1

Type and length

Deletion, 10 bp

Location

Cytogenetic: 2q37.1 2: 233768347-233768356 (GRCh38) [ NCBI UCSC ] 2: 234676993-234677002 (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	Apr 6, 2024	Apr 6, 2024	Mar 6, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000463.3:c.1216_1225del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000454.1:p.Thr406fs	frameshift
NM_001072.4:c.1213_1222del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001063.2:p.Thr405fs	frameshift
NM_007120.3:c.1219_1228del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_009051.1:p.Thr407fs	frameshift
NM_019075.4:c.1207_1216del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_061948.1:p.Thr403fs	frameshift
NM_019076.5:c.1207_1216del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_061949.3:p.Thr403fs	frameshift
NM_019077.3:c.1207_1216del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_061950.2:p.Thr403fs	frameshift
NM_019078.2:c.1219_1228del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_061951.1:p.Thr407fs	frameshift
NM_019093.4:c.1219_1228del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_061966.1:p.Thr407fs	frameshift
NM_021027.3:c.1207_1216del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_066307.1:p.Thr403fs	frameshift
NM_205862.3:c.412_421del	NP_995584.1:p.Thr138fs	frameshift
NC_000002.12:g.233768351_233768360del
NC_000002.11:g.234676997_234677006del
NG_002601.2:g.183608_183617del
NG_033238.1:g.13079_13088del
LRG_733:g.13079_13088del
LRG_733t1:c.1216_1225del	LRG_733p1:p.Thr406Leufs

... more HGVS ... less HGVS

Protein change

T138fs, T403fs, T405fs, T406fs, T407fs

Other names

Canonical SPDI

NC_000002.12:233768346:GGAGACTAAGGGAG:GGAG

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	-	589
UGT1A1		-	-	GRCh38 GRCh37	2	373
UGT1A10		-	-	GRCh38 GRCh37	-	591
UGT1A3		-	-	GRCh38 GRCh37	-	397
UGT1A4		-	-	GRCh38 GRCh37	-	423
UGT1A5		-	-	GRCh38 GRCh37	-	441
UGT1A6		-	-	GRCh38 GRCh37	-	484
UGT1A7		-	-	GRCh38 GRCh37	-	536
UGT1A8		-	-	GRCh38 GRCh37	-	619
UGT1A9		-	-	GRCh38 GRCh37	-	571

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.
Crigler-Najjar syndrome type 1 Crigler-Najjar syndrome, type II Gilbert syndrome Lucey-Driscoll syndrome	Pathogenic (1)	no assertion criteria provided	Mar 6, 2023	RCV003989472.1

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 (Mar 06, 2023)	no assertion criteria provided Method: clinical testing	Crigler-Najjar syndrome type 1 Crigler-Najjar syndrome, type II Lucey-Driscoll syndrome Gilbert syndrome Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: yes Allele origin: germline	Clinical Genetics Laboratory, University Hospital Schleswig-Holstein Accession: SCV004808349.1 First in ClinVar: Apr 06, 2024 Last updated: Apr 06, 2024

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.

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 Sep 01, 2024

ClinVar Genomic variation as it relates to human health

NM_000463.3(UGT1A1):c.1216_1225del (p.Thr406fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...