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NC_000004.11:g.(?_102001669)_(103806607_?)del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 13, 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:
RCV003105379.5

Allele description [Variation Report for NC_000004.11:g.(?_102001669)_(103806607_?)del]

NC_000004.11:g.(?_102001669)_(103806607_?)del

Genes:
  • BANK1:B cell scaffold protein with ankyrin repeats 1 [Gene - OMIM - HGNC]
  • CISD2:CDGSH iron sulfur domain 2 [Gene - OMIM - HGNC]
  • MANBA:mannosidase beta [Gene - OMIM - HGNC]
  • NFKB1:nuclear factor kappa B subunit 1 [Gene - OMIM - HGNC]
  • PPP3CA:protein phosphatase 3 catalytic subunit alpha [Gene - OMIM - HGNC]
  • SLC39A8:solute carrier family 39 member 8 [Gene - OMIM - HGNC]
  • SLC9B1:solute carrier family 9 member B1 [Gene - OMIM - HGNC]
  • UBE2D3:ubiquitin conjugating enzyme E2 D3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4q24
Genomic location:
Chr4: 102001669 - 103806607 (on Assembly GRCh37)
Preferred name:
NC_000004.11:g.(?_102001669)_(103806607_?)del
HGVS:
NC_000004.11:g.(?_102001669)_(103806607_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003794408Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 13, 2022) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures.

Myers CT, Stong N, Mountier EI, Helbig KL, Freytag S, Sullivan JE, Ben Zeev B, Nissenkorn A, Tzadok M, Heimer G, Shinde DN, Rezazadeh A, Regan BM, Oliver KL, Ernst ME, Lippa NC, Mulhern MS, Ren Z, Poduri A, Andrade DM, Bird LM, Bahlo M, et al.

Am J Hum Genet. 2017 Oct 5;101(4):516-524. doi: 10.1016/j.ajhg.2017.08.013. Epub 2017 Sep 21.

PubMed [citation]
PMID:
28942967
PMCID:
PMC5630160

Loss-of-function and gain-of-function mutations in PPP3CA cause two distinct disorders.

Mizuguchi T, Nakashima M, Kato M, Okamoto N, Kurahashi H, Ekhilevitch N, Shiina M, Nishimura G, Shibata T, Matsuo M, Ikeda T, Ogata K, Tsuchida N, Mitsuhashi S, Miyatake S, Takata A, Miyake N, Hata K, Kaname T, Matsubara Y, Saitsu H, Matsumoto N.

Hum Mol Genet. 2018 Apr 15;27(8):1421-1433. doi: 10.1093/hmg/ddy052.

PubMed [citation]
PMID:
29432562
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003794408.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PPP3CA-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 1-8 of the PPP3CA gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PPP3CA are known to be pathogenic (PMID: 28942967, 29432562, 30455226, 30951195).

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

Last Updated: Sep 29, 2024