NM_006031.6(PCNT):c.3594_3598dup (p.Leu1200fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 26, 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:: RCV003556271.1

Allele description [Variation Report for NM_006031.6(PCNT):c.3594_3598dup (p.Leu1200fs)]

NM_006031.6(PCNT):c.3594_3598dup (p.Leu1200fs)

Gene:

PCNT:pericentrin [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_006031.6(PCNT):c.3594_3598dup (p.Leu1200fs)

HGVS:

NC_000021.9:g.46388871_46388875dup
NG_008961.2:g.69750_69754dup
NM_001315529.2:c.3240_3244dup
NM_006031.6:c.3594_3598dupMANE SELECT
NP_001302458.1:p.Leu1082fs
NP_006022.3:p.Leu1200fs
NC_000021.8:g.47808785_47808786insGGCCC
NC_000021.8:g.47808786_47808790dup
NG_008961.1:g.69751_69755dup
NM_006031.5:c.3593_3594insGGCCC
NM_006031.5:c.3594_3598dupGGCCC

Protein change:

L1082fs

Links:

dbSNP: rs869312929

NCBI 1000 Genomes Browser:

rs869312929

Molecular consequence:

NM_001315529.2:c.3240_3244dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006031.6:c.3594_3598dup - 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
SCV004298823	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 26, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25356970, 18174396, 22821869, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004298823

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 26, 2023)

germline

clinical testing

PubMed (4)
[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

Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions.

Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Tippin Davis B, Baxter RM, Zeng W, Mroske C, Parra MC, Gandomi SK, Lu I, Li X, Lu H, Lu HM, Salvador D, Ruble D, Lao M, Fischbach S, Wen J, Lee S, Elliott A, et al.

Genet Med. 2015 Jul;17(7):578-86. doi: 10.1038/gim.2014.154. Epub 2014 Nov 13.

PubMed [citation]

PMID:: 25356970

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

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004298823.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 225019). This premature translational stop signal has been observed in individual(s) with PCNT-related conditions (PMID: 25356970). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu1200Argfs*47) 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).

#	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: Feb 20, 2024

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