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NM_005506.4(SCARB2):c.862C>T (p.Gln288Ter) AND Action myoclonus-renal failure syndrome

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
Oct 26, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000007803.14

Allele description [Variation Report for NM_005506.4(SCARB2):c.862C>T (p.Gln288Ter)]

NM_005506.4(SCARB2):c.862C>T (p.Gln288Ter)

Gene:
SCARB2:scavenger receptor class B member 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4q21.1
Genomic location:
Preferred name:
NM_005506.4(SCARB2):c.862C>T (p.Gln288Ter)
HGVS:
  • NC_000004.12:g.76174276G>A
  • NG_012054.1:g.44607C>T
  • NM_001204255.2:c.433C>T
  • NM_005506.4:c.862C>TMANE SELECT
  • NP_001191184.1:p.Gln145Ter
  • NP_005497.1:p.Gln288Ter
  • NP_005497.1:p.Gln288Ter
  • NC_000004.11:g.77095429G>A
  • NM_005506.3:c.862C>T
Protein change:
Q145*; GLN288TER
Links:
OMIM: 602257.0003; dbSNP: rs121909118
NCBI 1000 Genomes Browser:
rs121909118
Molecular consequence:
  • NM_001204255.2:c.433C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_005506.4:c.862C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Action myoclonus-renal failure syndrome
Synonyms:
MYOCLONUS-NEPHROPATHY SYNDROME; Epilepsy, progressive myoclonic 4, with or without renal failure; EPILEPSY, PROGRESSIVE MYOCLONIC, 4, WITH RENAL FAILURE; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009699; MeSH: D020191; MedGen: C0751779; Orphanet: 163696; OMIM: 254900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000028004OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 2011)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000328636GeneReviews
no classification provided
not providedgermlineliterature only

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

SCV002813619Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 18, 2022)
unknownclinical testing

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

SCV004122208Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Oct 26, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Action myoclonus-renal failure syndrome: characterization of a unique cerebro-renal disorder.

Badhwar A, Berkovic SF, Dowling JP, Gonzales M, Narayanan S, Brodtmann A, Berzen L, Caviness J, Trenkwalder C, Winkelmann J, Rivest J, Lambert M, Hernandez-Cossio O, Carpenter S, Andermann F, Andermann E.

Brain. 2004 Oct;127(Pt 10):2173-82. Epub 2004 Sep 13.

PubMed [citation]
PMID:
15364701

Progressive myoclonus epilepsy with demyelinating peripheral neuropathy and preserved intellect: a novel syndrome.

Costello DJ, Chiappa KH, Siao P.

Arch Neurol. 2009 Jul;66(7):898-901. doi: 10.1001/archneurol.2009.131.

PubMed [citation]
PMID:
19597094
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000028004.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

Berkovic et al. (2008) identified an SCARB2 mutation in 1 of the original families with action myoclonus with renal failure (EPM4; 254900) from Quebec reported by Badhwar et al. (2004). The 3 affected members were deceased, and no DNA was available for testing, but obligate carriers of this disorder had the mutation in exon 7 862C-T (gln288ter, Q288X), which was predicted to terminate the protein prematurely or lead to nonsense-mediated RNA decay of the transcript.

In a patient with progressive myoclonic epilepsy without renal failure, Dibbens et al. (2011) identified compound heterozygosity for 2 mutations in the SCARB2 gene: Q288X and a 1-bp insertion in intron 9 (1187+3insT; 602257.0007). The patient was originally reported by Costello et al. (2009). He had onset of myoclonic epilepsy at age 16 years, and became severely disabled, requiring a wheelchair by age 20. At age 27, he had intractable myoclonus, dysarthria, and dysphagia, but cognition remained intact and there was no evidence of renal failure. Electrophysiologic studies indicated a demyelinating peripheral neuropathy, with reduced sensory and motor action potentials and mildly decreased nerve conduction velocities.

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

From GeneReviews, SCV000328636.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002813619.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004122208.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Variant summary: SCARB2 c.862C>T (p.Gln288X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Variants downstream of this position have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 4e-06 in 251182 control chromosomes (gnomAD). c.862C>T has been reported in the literature in individuals affected with features of Action Myoclonus-Renal Failure Syndrome (examples: Berkovic_2008, and Li_2023). At least one publication reports experimental evidence that this variant disrupts the normal trafficking of the SCARB2 protein (Blanz_2010). The following publications have been ascertained in the context of this evaluation (PMID: 18308289, 19933215, 35478072). Three submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Oct 13, 2024