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NM_022356.4(P3H1):c.1080+1G>T AND P3H1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 18, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003914795.2

Allele description [Variation Report for NM_022356.4(P3H1):c.1080+1G>T]

NM_022356.4(P3H1):c.1080+1G>T

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.1080+1G>T
Other names:
P3H1, IVS5, G-T, +1
HGVS:
  • NC_000001.11:g.42757782C>A
  • NG_008123.1:g.14303G>T
  • NM_001146289.2:c.1080+1G>T
  • NM_001243246.2:c.1080+1G>T
  • NM_022356.4:c.1080+1G>TMANE SELECT
  • LRG_5t1:c.1080+1G>T
  • LRG_5:g.14303G>T
  • NC_000001.10:g.43223453C>A
  • NM_022356.3:c.1080+1G>T
Note:
NCBI staff reviewed the sequence information reported in PubMed 17277775 Fig. S1 to determine the location of this allele on the current reference sequence.
Nucleotide change:
IVS5, G-T, +1
Links:
OMIM: 610339.0001; dbSNP: rs72659351
NCBI 1000 Genomes Browser:
rs72659351
Molecular consequence:
  • NM_001146289.2:c.1080+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001243246.2:c.1080+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_022356.4:c.1080+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
P3H1-related disorder
Synonyms:
P3H1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004732219PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Jan 18, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004732219.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The P3H1 c.1080+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant is also referred to as IVS5+1G>T in the literature. It is a founder variant in individuals of West African descent and has been reported in the homozygous and compound heterozygous state in multiple individuals with autosomal recessive osteogenesis imperfecta (Cabral et al. 2007. PubMed ID: 17277775; Cabral et al. 2012. PubMed ID: 22281939; Fratzl-Zelman et al. 2016. PubMed ID: 27383115; Bardai et al. 2016. PubMed ID: 27509835; Santana et al. 2018. PubMed ID: 30246063; Trancozo et al. 2019. PubMed ID: 31429852). This variant is reported in 0.25% of alleles in individuals of African descent in gnomAD, which is consistent with this being a founder variant. Variants that disrupt the consensus splice donor site in P3H1 are expected to be pathogenic. This variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024