chr1-42762312-G-GT

Variant names:

• chr1-42762312-G-GT
• rs760593141
• ENST00000492956.1:n.674dupA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The ENST00000492956.1(P3H1):​n.674dupA variant causes a non coding transcript exon 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 ENST00000492956.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 8

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• osteogenesis imperfecta type 2

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• osteogenesis imperfecta type 3

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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 CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GT is described in CliVar as Benign. Clinvar id is 2803701.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
P3H1	NM_022356.4	c.618+10dupA		intron_variant	Intron 2 of 14	ENST00000296388.10	NP_071751.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
P3H1	ENST00000296388.10	c.618+10dupA		intron_variant	Intron 2 of 14	1	NM_022356.4	ENSP00000296388.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1458684 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 725840

African (AFR) AF: 0.00 AC: 0 AN: 33406

American (AMR) AF: 0.00 AC: 0 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26100

East Asian (EAS) AF: 0.00 AC: 0 AN: 39664

South Asian (SAS) AF: 0.00 AC: 0 AN: 86204

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53360

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5762

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1109212

Other (OTH) AF: 0.00 AC: 0 AN: 60264

GnomAD4 genome Cov.: 32

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Osteogenesis imperfecta type 8 Benign:1

Jun 28, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs760593141; hg19: chr1-43227983;