NM_000463.3(UGT1A1):c.1220del (p.Lys407fs) AND Crigler-Najjar syndrome, type II

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 10, 2019
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:: RCV002466687.8

Allele description [Variation Report for NM_000463.3(UGT1A1):c.1220del (p.Lys407fs)]

NM_000463.3(UGT1A1):c.1220del (p.Lys407fs)

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:

Deletion

Cytogenetic location:

2q37.1

Genomic location:

Preferred name:

NM_000463.3(UGT1A1):c.1220del (p.Lys407fs)

HGVS:

NC_000002.12:g.233768355del
NG_002601.2:g.183612del
NG_033238.1:g.13083del
NM_000463.3:c.1220delMANE SELECT
NM_001072.4:c.1217delMANE SELECT
NM_007120.3:c.1223delMANE SELECT
NM_019075.4:c.1211delMANE SELECT
NM_019076.5:c.1211delMANE SELECT
NM_019077.3:c.1211delMANE SELECT
NM_019078.2:c.1223delMANE SELECT
NM_019093.4:c.1223delMANE SELECT
NM_021027.3:c.1211delMANE SELECT
NM_205862.3:c.416del
NP_000454.1:p.Lys407fs
NP_001063.2:p.Lys406fs
NP_009051.1:p.Lys408fs
NP_061948.1:p.Lys404fs
NP_061949.3:p.Lys404fs
NP_061950.2:p.Lys404fs
NP_061951.1:p.Lys408fs
NP_061966.1:p.Lys408fs
NP_066307.1:p.Lys404fs
NP_995584.1:p.Lys139fs
LRG_733t1:c.1220del
LRG_733:g.13083del
NC_000002.11:g.234677000del
NC_000002.11:g.234677001del
NM_000463.2:c.1220del
NM_000463.2:c.1220delA

Protein change:

K139fs

Links:

dbSNP: rs558109660

NCBI 1000 Genomes Browser:

rs558109660

Molecular consequence:

NM_000463.3:c.1220del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001072.4:c.1217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_007120.3:c.1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_019075.4:c.1211del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_019076.5:c.1211del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_019077.3:c.1211del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_019078.2:c.1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_019093.4:c.1223del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_021027.3:c.1211del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_205862.3:c.416del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Crigler-Najjar syndrome, type II
Synonyms:: HYPERBILIRUBINEMIA, CRIGLER-NAJJAR TYPE II; Crigler Najjar syndrome, type 2; Mutation in the UDP-glucuronosyl-transferase gene
Identifiers:: MONDO: MONDO:0011725; MedGen: C2931132; Orphanet: 205; OMIM: 606785

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002761595	Genetics and Molecular Pathology, SA Pathology See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 10, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002761595

Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 10, 2019)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genetics and Molecular Pathology, SA Pathology, SCV002761595.1

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

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

Last Updated: May 1, 2024

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