NM_000100.4(CSTB):c.64C>T (p.Gln22Ter) AND Progressive myoclonic epilepsy

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 3, 2018
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:: RCV000697295.5

Allele description [Variation Report for NM_000100.4(CSTB):c.64C>T (p.Gln22Ter)]

NM_000100.4(CSTB):c.64C>T (p.Gln22Ter)

Genes:

LOC130066788:ATAC-STARR-seq lymphoblastoid silent region 13368 [Gene]
CSTB:cystatin B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_000100.4(CSTB):c.64C>T (p.Gln22Ter)

HGVS:

NC_000021.9:g.43776206G>A
NG_011545.1:g.5173C>T
NM_000100.4:c.64C>TMANE SELECT
NP_000091.1:p.Gln22Ter
NP_000091.1:p.Gln22Ter
LRG_485t1:c.64C>T
LRG_485:g.5173C>T
LRG_485p1:p.Gln22Ter
NC_000021.8:g.45196087G>A
NM_000100.3:c.64C>T

Protein change:

Q22*

Links:

dbSNP: rs1569006250

NCBI 1000 Genomes Browser:

rs1569006250

Molecular consequence:

NM_000100.4:c.64C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Progressive myoclonic epilepsy
Synonyms:: Myoclonic Epilepsies, Progressive; Familial progressive myoclonic epilepsy; Progressive myoclonus epilepsy; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0020074; MedGen: C0751778; Orphanet: 308; OMIM: PS254800

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000825895	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 3, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 8596935, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000825895

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 3, 2018)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Mutations in the gene encoding cystatin B in progressive myoclonus epilepsy (EPM1)

Pennacchio LA, Lehesjoki AE, Stone NE, Willour VL, Virtaneva K, Miao J, D'Amato E, Ramirez L, Faham M, Koskiniemi M, Warrington JA, Norio R, de la Chapelle A, Cox DR, Myers RM.

Science. 1996 Mar 22;271(5256):1731-4.

PubMed [citation]

PMID:: 8596935

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000825895.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Gln22*) in the CSTB gene. It is expected to result in an absent or disrupted protein product. While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with CSTB-related disease. Loss-of-function variants in CSTB are known to be pathogenic (PMID: 8596935). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024

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