NM_001384732.1(CPLANE1):c.1419_1420insTC (p.Leu475fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 17, 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:: RCV001919397.4

Allele description [Variation Report for NM_001384732.1(CPLANE1):c.1419_1420insTC (p.Leu475fs)]

NM_001384732.1(CPLANE1):c.1419_1420insTC (p.Leu475fs)

Gene:

CPLANE1:ciliogenesis and planar polarity effector complex subunit 1 [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

5p13.2

Genomic location:

Preferred name:

NM_001384732.1(CPLANE1):c.1419_1420insTC (p.Leu475fs)

HGVS:

NC_000005.10:g.37227344_37227345insGA
NG_032772.2:g.27084_27085insTC
NM_001384732.1:c.1419_1420insTCMANE SELECT
NM_023073.4:c.1419_1420insTC
NP_001371661.1:p.Leu475fs
NP_075561.3:p.Leu475fs
NC_000005.9:g.37227446_37227447insGA

Protein change:

L475fs

Links:

dbSNP: rs2150448548

NCBI 1000 Genomes Browser:

rs2150448548

Molecular consequence:

NM_001384732.1:c.1419_1420insTC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_023073.4:c.1419_1420insTC - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Mus musculus growth differentiation factor 9 (Gdf9), transcript variant 1, mRNA
Mus musculus growth differentiation factor 9 (Gdf9), transcript variant 1, mRNA
gi|160298181|ref|NM_008110.2|

Nucleotide
P20 protein, partial [Bamboo mosaic virus satellite RNA]
P20 protein, partial [Bamboo mosaic virus satellite RNA]
gi|757006882|gb|AJN57845.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002191888	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 17, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24178751, 26092869, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002191888

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 17, 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

C5orf42 is the major gene responsible for OFD syndrome type VI.

Lopez E, Thauvin-Robinet C, Reversade B, Khartoufi NE, Devisme L, Holder M, Ansart-Franquet H, Avila M, Lacombe D, Kleinfinger P, Kaori I, Takanashi J, Le Merrer M, Martinovic J, Noël C, Shboul M, Ho L, Güven Y, Razavi F, Burglen L, Gigot N, Darmency-Stamboul V, et al.

Hum Genet. 2014 Mar;133(3):367-77. doi: 10.1007/s00439-013-1385-1. Epub 2013 Nov 1.

PubMed [citation]

PMID:: 24178751

Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity.

Bachmann-Gagescu R, Dempsey JC, Phelps IG, O'Roak BJ, Knutzen DM, Rue TC, Ishak GE, Isabella CR, Gorden N, Adkins J, Boyle EA, de Lacy N, O'Day D, Alswaid A, Ramadevi A R, Lingappa L, Lourenço C, Martorell L, Garcia-Cazorla À, Ozyürek H, Haliloğlu G, Tuysuz B, et al.

J Med Genet. 2015 Aug;52(8):514-22. doi: 10.1136/jmedgenet-2015-103087. Epub 2015 Jun 19.

PubMed [citation]

PMID:: 26092869
PMCID:: PMC5082428

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002191888.3

#	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.Leu475Alafs*3) in the CPLANE1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CPLANE1 are known to be pathogenic (PMID: 24178751, 26092869). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CPLANE1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1422168). For these reasons, this variant has been classified as Pathogenic.

#	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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