3-189957981-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_018192.4(P3H2):c.2058G>A(p.Val686Val) variant causes a synonymous change. The variant allele was found at a frequency of 0.000000684 in 1,461,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
P3H2
NM_018192.4 synonymous
NM_018192.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.67
Publications
1 publications found
Genes affected
P3H2 (HGNC:19317): (prolyl 3-hydroxylase 2) This gene encodes a member of the prolyl 3-hydroxylase subfamily of 2-oxo-glutarate-dependent dioxygenases. These enzymes play a critical role in collagen chain assembly, stability and cross-linking by catalyzing post-translational 3-hydroxylation of proline residues. Mutations in this gene are associated with nonsyndromic severe myopia with cataract and vitreoretinal degeneration, and downregulation of this gene may play a role in breast cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
P3H2 Gene-Disease associations (from GenCC):
- myopia, high, with cataract and vitreoretinal degenerationInheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 3-189957981-C-T is Benign according to our data. Variant chr3-189957981-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3674621.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_018192.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| P3H2 | NM_018192.4 | MANE Select | c.2058G>A | p.Val686Val | synonymous | Exon 15 of 15 | NP_060662.2 | ||
| P3H2 | NM_001134418.2 | c.1515G>A | p.Val505Val | synonymous | Exon 15 of 15 | NP_001127890.1 | Q8IVL5-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| P3H2 | ENST00000319332.10 | TSL:1 MANE Select | c.2058G>A | p.Val686Val | synonymous | Exon 15 of 15 | ENSP00000316881.5 | Q8IVL5-1 | |
| P3H2 | ENST00000427335.6 | TSL:1 | c.1515G>A | p.Val505Val | synonymous | Exon 15 of 15 | ENSP00000408947.2 | Q8IVL5-2 | |
| P3H2 | ENST00000895815.1 | c.2127G>A | p.Val709Val | synonymous | Exon 15 of 15 | ENSP00000565874.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461358Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727052 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461358
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
727052
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33470
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39690
South Asian (SAS)
AF:
AC:
0
AN:
86254
European-Finnish (FIN)
AF:
AC:
0
AN:
53404
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111548
Other (OTH)
AF:
AC:
0
AN:
60368
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
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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