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NM_002655.3(PLAG1):c.441_489del (p.Ser147fs) AND Silver-russell syndrome 4

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 22, 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:
RCV002251292.1

Allele description [Variation Report for NM_002655.3(PLAG1):c.441_489del (p.Ser147fs)]

NM_002655.3(PLAG1):c.441_489del (p.Ser147fs)

Genes:
LOC126860395:BRD4-independent group 4 enhancer GRCh37_chr8:57079228-57080427 [Gene]
PLAG1:PLAG1 zinc finger [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
8q12.1
Genomic location:
Preferred name:
NM_002655.3(PLAG1):c.441_489del (p.Ser147fs)
HGVS:
  • NC_000008.11:g.56167257_56167305del
  • NG_023310.1:g.48996_49044del
  • NM_001114634.2:c.441_489del
  • NM_001114635.2:c.195_243del
  • NM_002655.3:c.441_489delMANE SELECT
  • NP_001108106.1:p.Ser147fs
  • NP_001108107.1:p.Ser65fs
  • NP_002646.2:p.Ser147fs
  • NC_000008.10:g.57079816_57079864del
Protein change:
S147fs
Links:
dbSNP: rs2129224609
NCBI 1000 Genomes Browser:
rs2129224609
Molecular consequence:
  • NM_001114634.2:c.441_489del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001114635.2:c.195_243del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002655.3:c.441_489del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Silver-russell syndrome 4
Identifiers:
MONDO: MONDO:0030118; MedGen: C5394450; OMIM: 618907

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0025218883billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(May 22, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not 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 3billion, SCV002521888.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The deletion creates a frameshift variant within 50 bp downstream of the penultimate exon or last exon. While it is expected to escape nonsense-mediated mRNA decay, the truncated region is considered critical because most of the pathogenic variants previously reported have been found in this region. It is absent from the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Dec 24, 2023