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NM_198334.3(GANAB):c.2830C>T (p.Arg944Ter) AND Polycystic kidney disease 3 with or without polycystic liver disease

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 26, 2020
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:
RCV002273080.3

Allele description [Variation Report for NM_198334.3(GANAB):c.2830C>T (p.Arg944Ter)]

NM_198334.3(GANAB):c.2830C>T (p.Arg944Ter)

Gene:
GANAB:glucosidase II alpha subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q12.3
Genomic location:
Preferred name:
NM_198334.3(GANAB):c.2830C>T (p.Arg944Ter)
HGVS:
  • NC_000011.10:g.62625820G>A
  • NG_031863.1:g.1356C>T
  • NG_053018.1:g.25907C>T
  • NM_001278192.2:c.2554C>T
  • NM_001278193.2:c.2488C>T
  • NM_001278194.2:c.2539C>T
  • NM_001329222.2:c.2539C>T
  • NM_001329223.2:c.2539C>T
  • NM_001329224.2:c.2107C>T
  • NM_001329225.2:c.2107C>T
  • NM_198334.3:c.2830C>TMANE SELECT
  • NM_198335.4:c.2896C>T
  • NP_001265121.1:p.Arg852Ter
  • NP_001265122.1:p.Arg830Ter
  • NP_001265123.1:p.Arg847Ter
  • NP_001316151.1:p.Arg847Ter
  • NP_001316152.1:p.Arg847Ter
  • NP_001316153.1:p.Arg703Ter
  • NP_001316154.1:p.Arg703Ter
  • NP_938148.1:p.Arg944Ter
  • NP_938149.2:p.Arg966Ter
  • NC_000011.9:g.62393292G>A
  • NM_198334.2:c.2830C>T
Protein change:
R703*
Links:
dbSNP: rs781470089
NCBI 1000 Genomes Browser:
rs781470089
Molecular consequence:
  • NM_001278192.2:c.2554C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278193.2:c.2488C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278194.2:c.2539C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001329222.2:c.2539C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001329223.2:c.2539C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001329224.2:c.2107C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001329225.2:c.2107C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_198334.3:c.2830C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_198335.4:c.2896C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Polycystic kidney disease 3 with or without polycystic liver disease
Synonyms:
POLYCYSTIC KIDNEY DISEASE, ADULT, TYPE III; Polycystic kidney disease 3
Identifiers:
MONDO: MONDO:0010916; MedGen: C3887964; OMIM: 600666

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002557675Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 26, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557675.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as a 3B-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. NMD-predicted variants resulting in loss of protein function have previously been reported in this gene, however the mechanism for a truncating variant is currently unknown (ClinVar). (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0205 - Variant is predicted to result in a truncated protein with less than 1/3 of the protein affected (exon 24 of 24). (P) 0251 - Variant is heterozygous. (N) 0302 - Variant is present in gnomAD <0.001 for a dominant condition (7 heterozygotes, 0 homozygotes). (P) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (N) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 23, 2024