NM_022356.4(P3H1):c.1647G>A (p.Met549Ile) AND Osteogenesis imperfecta type 8

Germline classification:: Benign (2 submissions)
Last evaluated:: Feb 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001095988.10

Allele description [Variation Report for NM_022356.4(P3H1):c.1647G>A (p.Met549Ile)]

NM_022356.4(P3H1):c.1647G>A (p.Met549Ile)

Gene:

P3H1:prolyl 3-hydroxylase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_022356.4(P3H1):c.1647G>A (p.Met549Ile)

HGVS:

NC_000001.11:g.42750259C>T
NG_008123.1:g.21826G>A
NM_001146289.2:c.1647G>A
NM_001243246.2:c.1647G>A
NM_022356.4:c.1647G>AMANE SELECT
NP_001139761.1:p.Met549Ile
NP_001230175.1:p.Met549Ile
NP_071751.3:p.Met549Ile
NP_071751.3:p.Met549Ile
LRG_5t1:c.1647G>A
LRG_5:g.21826G>A
LRG_5p1:p.Met549Ile
NC_000001.10:g.43215930C>T
NM_022356.3:c.1647G>A

Protein change:

M549I

Links:

dbSNP: rs11581921

NCBI 1000 Genomes Browser:

rs11581921

Molecular consequence:

NM_001146289.2:c.1647G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243246.2:c.1647G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_022356.4:c.1647G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001252168	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 28, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001726416	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001252168

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 28, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV001726416

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Feb 1, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Mutational characterization of the P3H1/CRTAP/CypB complex in recessive osteogenesis imperfecta.

Barbirato C, Trancozo M, Almeida MG, Almeida LS, Santos TO, Duarte JC, Rebouças MR, Sipolatti V, Nunes VR, Paula F.

Genet Mol Res. 2015 Dec 3;14(4):15848-58. doi: 10.4238/2015.December.1.36.

PubMed [citation]

PMID:: 26634552

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001252168.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	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

From Invitae, SCV001726416.4

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

#	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 28, 2024

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