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NM_006031.6(PCNT):c.5767C>T (p.Arg1923Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Feb 21, 2021)
Last evaluated:
Feb 12, 2020
Accession:
VCV000004706.3
Variation ID:
4706
Description:
single nucleotide variant
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NM_006031.6(PCNT):c.5767C>T (p.Arg1923Ter)

Allele ID
19745
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
21q22.3
Genomic location
21: 46411840 (GRCh38) GRCh38 UCSC
21: 47831754 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000021.8:g.47831754C>T
NC_000021.9:g.46411840C>T
NG_008961.1:g.92719C>T
... more HGVS
Protein change
R1923*, R1805*
Other names
-
Canonical SPDI
NC_000021.9:46411839:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA250510
OMIM: 605925.0004
dbSNP: rs119479062
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Feb 12, 2020 RCV000004971.8
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PCNT - - GRCh38
GRCh37
999 1099

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Mar 05, 2013)
criteria provided, single submitter
Method: clinical testing
Microcephalic osteodysplastic primordial dwarfism, type II
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000194518.1
Submitted: (Sep 11, 2014)
Evidence details
Likely pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Microcephalic osteodysplastic primordial dwarfism type II
Allele origin: germline
Pathology and Clinical Laboratory Medicine,King Fahad Medical City
Accession: SCV001438861.1
Submitted: (May 26, 2020)
Evidence details
Pathogenic
(Feb 12, 2020)
criteria provided, single submitter
Method: clinical testing
Microcephalic osteodysplastic primordial dwarfism type II
Allele origin: unknown
Baylor Genetics
Accession: SCV001523583.1
Submitted: (Feb 21, 2021)
Evidence details
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Pathogenic
(Feb 08, 2008)
no assertion criteria provided
Method: literature only
MICROCEPHALIC OSTEODYSPLASTIC PRIMORDIAL DWARFISM, TYPE II
Allele origin: germline
OMIM
Accession: SCV000025147.4
Submitted: (Aug 18, 2015)
Evidence details
Publications
PubMed (3)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Mutations in the pericentrin (PCNT) gene cause primordial dwarfism. Rauch A Science (New York, N.Y.) 2008 PMID: 18174396
Microcephalic osteodysplastic primordial dwarfism with severe microdontia and skin anomalies: confirmation of a new syndrome. Kantaputra PN American journal of medical genetics. Part A 2004 PMID: 15372530
Apparently new osteodysplastic and primordial short stature with severe microdontia, opalescent teeth, and rootless molars in two siblings. Kantaputra PN American journal of medical genetics 2002 PMID: 12210304

Text-mined citations for rs119479062...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021