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NM_006031.6(PCNT):c.3465-1G>A AND Microcephalic osteodysplastic primordial dwarfism type II

Germline classification:
Likely pathogenic (5 submissions)
Last evaluated:
Jan 1, 2019
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:
RCV000758566.7

Allele description [Variation Report for NM_006031.6(PCNT):c.3465-1G>A]

NM_006031.6(PCNT):c.3465-1G>A

Gene:
PCNT:pericentrin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.3
Genomic location:
Preferred name:
NM_006031.6(PCNT):c.3465-1G>A
HGVS:
  • NC_000021.9:g.46388741G>A
  • NG_008961.2:g.69620G>A
  • NM_001315529.2:c.3111-1G>A
  • NM_006031.6:c.3465-1G>AMANE SELECT
  • NC_000021.8:g.47808656G>A
  • NM_006031.5:c.3465-1G>A
Nucleotide change:
IVS17AS, G-A, -1
Links:
OMIM: 605925.0013; dbSNP: rs755084205
NCBI 1000 Genomes Browser:
rs755084205
Molecular consequence:
  • NM_001315529.2:c.3111-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_006031.6:c.3465-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
Functional consequence:
cryptic splice acceptor activation [Variation Ontology: 0375]
Observations:
3

Condition(s)

Name:
Microcephalic osteodysplastic primordial dwarfism type II (MOPD2)
Synonyms:
MOPD II; OSTEODYSPLASTIC PRIMORDIAL DWARFISM, TYPE II; Microcephalic osteodysplastic primordial dwarfism type 2; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008872; MedGen: C0432246; Orphanet: 2637; OMIM: 210720

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000886545The Genetics Institute, Rambam Health Care Campus
no assertion criteria provided
Pathogenicinheritedclinical testing

SCV001432321Service de Génétique Moléculaire, Hôpital Robert Debré
no assertion criteria provided
Likely pathogenicunknownclinical testing

SCV001440981Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 1, 2019)
unknownclinical testing

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

SCV001478377OMIM
no assertion criteria provided
Pathogenic
(Feb 2, 2021)
germlineliterature only

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

SCV002073953GeneReviews
no classification provided
not providedgermlineliterature only

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot provided1not providednot providednot providedclinical testing
Druzeinheritedyes22not 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

Identification of a novel PCNT founder pathogenic variant in the Israeli Druze population.

Weiss K, Ekhilevitch N, Cohen L, Bratman-Morag S, Bello R, Martinez AF, Hadid Y, Shlush LI, Kurolap A, Paperna T, Mory A, Baris HN, Muenke M.

Eur J Med Genet. 2020 Feb;63(2):103643. doi: 10.1016/j.ejmg.2019.03.007. Epub 2019 Mar 25.

PubMed [citation]
PMID:
30922925

Details of each submission

From The Genetics Institute, Rambam Health Care Campus, SCV000886545.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Druze2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided2not provided2not provided

From Service de Génétique Moléculaire, Hôpital Robert Debré, SCV001432321.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot provided1not provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440981.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From OMIM, SCV001478377.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 2 unrelated patients from the Druze population in Israel with microcephalic osteodysplastic primordial dwarfism type II (MOPD2; 210720), Weiss et al. (2020) identified homozygosity for a G-A transition in the -1 position of intron 17 (c.3465-1G-A, NM_006031.5) of the PCNT gene. In patient 1 the mutation was identified by whole-exome sequencing, and in patient 2 it was identified by direct sequencing of the PCNT gene. The parents of patient 1 were mutation carriers. The c.3465-1G-A mutation was reported in heterozygous state in 4 individuals from South Asia in the gnomAD database (allele frequency of 0.0001) and was not present in the Greater Middle East Variome Project database. Sequencing of lymphoblastoid cell cDNA from patient 1 and his parents revealed a 2-bp deletion at the beginning of exon 18 due to the activation of a cryptic splice site, resulting in a frameshift and premature termination (Ala1157ProfsTer36). Weiss et al. (2020) concluded that this is a founder mutation.

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

From GeneReviews, SCV002073953.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

Founder variant in Israeli Druze population

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

Last Updated: Jun 23, 2024