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NM_145239.3(PRRT2):c.67G>A (p.Glu23Lys) AND multiple conditions

Germline classification:
Likely benign (1 submission)
Last evaluated:
Oct 24, 2022
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:
RCV003224153.8

Allele description [Variation Report for NM_145239.3(PRRT2):c.67G>A (p.Glu23Lys)]

NM_145239.3(PRRT2):c.67G>A (p.Glu23Lys)

Genes:
MVP-DT:MVP divergent transcript [Gene - HGNC]
PRRT2:proline rich transmembrane protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p11.2
Genomic location:
Preferred name:
NM_145239.3(PRRT2):c.67G>A (p.Glu23Lys)
HGVS:
  • NC_000016.10:g.29813121G>A
  • NG_032039.1:g.6034G>A
  • NM_001256442.1:c.67G>A
  • NM_001256442.2:c.67G>A
  • NM_001256443.2:c.67G>A
  • NM_145239.3:c.67G>AMANE SELECT
  • NP_001243371.1:p.Glu23Lys
  • NP_001243372.1:p.Glu23Lys
  • NP_660282.2:p.Glu23Lys
  • NC_000016.9:g.29824442G>A
  • NM_145239.2:c.67G>A
Protein change:
E23K
Links:
dbSNP: rs140383655
NCBI 1000 Genomes Browser:
rs140383655
Molecular consequence:
  • NM_001256442.2:c.67G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256443.2:c.67G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_145239.3:c.67G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Seizures, benign familial infantile, 2 (BFIS2)
Synonyms:
CONVULSIONS, BENIGN FAMILIAL INFANTILE, 2
Identifiers:
MONDO: MONDO:0011593; MedGen: C1853995; Orphanet: 306; OMIM: 605751
Name:
Episodic kinesigenic dyskinesia 1 (EKD1)
Synonyms:
Dystonia 10; Paroxysmal kinesigenic choreoathetosis; PxMD-PRRT2; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0100352; MedGen: C4552000; Orphanet: 98809; OMIM: 128200
Name:
Infantile convulsions and choreoathetosis (ICCA)
Synonyms:
Infantile convulsions and paroxysmal choreoathetosis, familial; Convulsions, infantile, with paroxysmal choreoathetosis, familial; PAROXYSMAL KINESIGENIC DYSKINESIA WITH INFANTILE CONVULSIONS
Identifiers:
MONDO: MONDO:0011178; MedGen: C1865926; Orphanet: 31709; OMIM: 602066

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003920358Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Oct 24, 2022) 		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 Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003920358.1

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

Description

PRRT2 NM_145239.2 exon 2 p.Glu23Lys (c.67G>A): This variant has not been reported in the literature but is present in 0.1% (132/68016) of European alleles including 1 homozygote in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/16-29813121-G-A?dataset=gnomad_r3). This variant is present in ClinVar, with several labs classifying this variant as Likely Benign or Benign (Variation ID:130039). This variant amino acid Lysine (Lys) is present in several species and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant suggests that this variant does not cause disease, but requires further evidence. Therefore this variant is classified as likely benign.

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

Last Updated: Oct 26, 2024