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NM_001135629.3(PPP1R21):c.1171del (p.Lys390_Met391insTer) AND Neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 3, 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:
RCV001807954.1

Allele description [Variation Report for NM_001135629.3(PPP1R21):c.1171del (p.Lys390_Met391insTer)]

NM_001135629.3(PPP1R21):c.1171del (p.Lys390_Met391insTer)

Gene:
PPP1R21:protein phosphatase 1 regulatory subunit 21 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_001135629.3(PPP1R21):c.1171del (p.Lys390_Met391insTer)
HGVS:
  • NC_000002.12:g.48474765del
  • NM_001135629.3:c.1171delMANE SELECT
  • NM_001193475.2:c.1171del
  • NM_152994.5:c.1171del
  • NP_001129101.1:p.Lys390_Met391insTer
  • NP_001180404.1:p.Lys390_Met391insTer
  • NP_694539.1:p.Lys390_Met391insTer
  • NC_000002.11:g.48701904del
  • NR_024188.3:n.1398del
Links:
dbSNP: rs2103865102
NCBI 1000 Genomes Browser:
rs2103865102
Molecular consequence:
  • NR_024188.3:n.1398del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001135629.3:c.1171del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001193475.2:c.1171del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152994.5:c.1171del - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities (NEDHFBA)
Identifiers:
MONDO: MONDO:0859165; MedGen: C5543591; OMIM: 619383

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0020582703billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jan 3, 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, SCV002058270.1

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

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is not observed in 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