chr1-42762312-G-GT
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_022356.4(P3H1):c.618+10dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
P3H1
NM_022356.4 intron
NM_022356.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.435
Publications
0 publications found
Genes affected
P3H1 (HGNC:19316): (prolyl 3-hydroxylase 1) This gene encodes an enzyme that is a member of the collagen prolyl hydroxylase family. These enzymes are localized to the endoplasmic reticulum and their activity is required for proper collagen synthesis and assembly. Mutations in this gene are associated with osteogenesis imperfecta type VIII. Three alternatively spliced transcript variants encoding different isoforms have been described. Other variants may exist, but their biological validity has not been determined. [provided by RefSeq, Aug 2011]
P3H1 Gene-Disease associations (from GenCC):
- osteogenesis imperfecta type 8Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- osteogenesis imperfecta type 2Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- osteogenesis imperfecta type 3Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 1-42762312-G-GT is Benign according to our data. Variant chr1-42762312-G-GT is described in ClinVar as Benign. ClinVar VariationId is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_022356.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| P3H1 | TSL:1 MANE Select | c.618+10dupA | intron | N/A | ENSP00000296388.5 | Q32P28-1 | |||
| P3H1 | TSL:1 | c.618+10dupA | intron | N/A | ENSP00000380245.3 | Q32P28-4 | |||
| P3H1 | TSL:1 | n.674dupA | non_coding_transcript_exon | Exon 2 of 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1458684Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 725840
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1458684
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
725840
African (AFR)
AF:
AC:
0
AN:
33406
American (AMR)
AF:
AC:
0
AN:
44712
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26100
East Asian (EAS)
AF:
AC:
0
AN:
39664
South Asian (SAS)
AF:
AC:
0
AN:
86204
European-Finnish (FIN)
AF:
AC:
0
AN:
53360
Middle Eastern (MID)
AF:
AC:
0
AN:
5762
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1109212
Other (OTH)
AF:
AC:
0
AN:
60264
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Osteogenesis imperfecta type 8 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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