NC_000001.10:g.(?_43212368)_(43223613_?)del AND Osteogenesis imperfecta type 8

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:: RCV004584070.2

Allele description [Variation Report for NC_000001.10:g.(?_43212368)_(43223613_?)del]

NC_000001.10:g.(?_43212368)_(43223613_?)del

Gene:: P3H1:prolyl 3-hydroxylase 1 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 1p34.2
Genomic location:: Chr1: 43212368 - 43223613 (on Assembly GRCh37)
Preferred name:: NC_000001.10:g.(?_43212368)_(43223613_?)del
HGVS:: NC_000001.10:g.(?_43212368)_(43223613_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Osteogenesis imperfecta type 8 (OI8)
Synonyms:: OI type VIII
Identifiers:: MONDO: MONDO:0012581; MedGen: C1970458; OMIM: 610915

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Coriell GM19908
Coriell GM19908

biosample
Lipa lipase A, lysosomal acid type [Rattus norvegicus]
Lipa lipase A, lysosomal acid type [Rattus norvegicus]
Gene ID:25055

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005066463	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 26, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22615817, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005066463

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 26, 2023)

unknown

clinical testing

PubMed (2)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A novel mutation in LEPRE1 that eliminates only the KDEL ER- retrieval sequence causes non-lethal osteogenesis imperfecta.

Takagi M, Ishii T, Barnes AM, Weis M, Amano N, Tanaka M, Fukuzawa R, Nishimura G, Eyre DR, Marini JC, Hasegawa T.

PLoS One. 2012;7(5):e36809. doi: 10.1371/journal.pone.0036809. Epub 2012 May 15.

PubMed [citation]

PMID:: 22615817
PMCID:: PMC3352923

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005066463.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant has not been reported in the literature in individuals affected with P3H1-related conditions. For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the P3H1 protein in which other variant(s) (p.Glu719Argfs*11) have been determined to be pathogenic (PMID: 22615817). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant is a gross deletion of the genomic region encompassing exon(s) 5-15 of the P3H1 gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product.

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

Last Updated: Sep 29, 2024

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