NM_006031.6(PCNT):c.3113_3143del (p.Val1038fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 19, 2023
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:: RCV003839166.2

Allele description [Variation Report for NM_006031.6(PCNT):c.3113_3143del (p.Val1038fs)]

NM_006031.6(PCNT):c.3113_3143del (p.Val1038fs)

Gene:

PCNT:pericentrin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_006031.6(PCNT):c.3113_3143del (p.Val1038fs)

HGVS:

NC_000021.9:g.46367087_46367117del
NG_008961.2:g.47966_47996del
NM_001315529.2:c.2759_2789del
NM_006031.6:c.3113_3143delMANE SELECT
NP_001302458.1:p.Val920fs
NP_006022.3:p.Val1038fs
NC_000021.8:g.47787002_47787032del

Protein change:

V1038fs

Molecular consequence:

NM_001315529.2:c.2759_2789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006031.6:c.3113_3143del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004636337	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 19, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18174396, 22821869, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004636337

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 19, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in the pericentrin (PCNT) gene cause primordial dwarfism.

Rauch A, Thiel CT, Schindler D, Wick U, Crow YJ, Ekici AB, van Essen AJ, Goecke TO, Al-Gazali L, Chrzanowska KH, Zweier C, Brunner HG, Becker K, Curry CJ, Dallapiccola B, Devriendt K, Dörfler A, Kinning E, Megarbane A, Meinecke P, Semple RK, Spranger S, et al.

Science. 2008 Feb 8;319(5864):816-9. doi: 10.1126/science.1151174. Epub 2008 Jan 3.

PubMed [citation]

PMID:: 18174396

Growth in individuals with Majewski osteodysplastic primordial dwarfism type II caused by pericentrin mutations.

Bober MB, Niiler T, Duker AL, Murray JE, Ketterer T, Harley ME, Alvi S, Flora C, Rustad C, Bongers EM, Bicknell LS, Wise C, Jackson AP.

Am J Med Genet A. 2012 Nov;158A(11):2719-25. doi: 10.1002/ajmg.a.35447. Epub 2012 Jul 20.

PubMed [citation]

PMID:: 22821869

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004636337.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Val1038Alafs*58) in the PCNT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCNT are known to be pathogenic (PMID: 18174396, 22821869). This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PCNT-related conditions.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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