rs3062112
Your query was ambiguous. Multiple possible variants found:
- chr3-189957700-AAGAGAGAGAG-A
- chr3-189957700-AAGAGAGAGAG-AAG
- chr3-189957700-AAGAGAGAGAG-AAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAGAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAGAGAGAGAGAGAGAG
- chr3-189957700-AAGAGAGAGAG-AAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018192.4(P3H2):c.*202_*211delCTCTCTCTCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000092 in 543,284 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000068 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
P3H2
NM_018192.4 3_prime_UTR
NM_018192.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.38
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
P3H2 | ENST00000319332 | c.*202_*211delCTCTCTCTCT | 3_prime_UTR_variant | Exon 15 of 15 | 1 | NM_018192.4 | ENSP00000316881.5 | |||
P3H2 | ENST00000427335 | c.*202_*211delCTCTCTCTCT | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000408947.2 | ||||
P3H2 | ENST00000490940.1 | n.459_468delCTCTCTCTCT | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000678 AC: 1AN: 147502Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000101 AC: 4AN: 395782Hom.: 0 AF XY: 0.0000141 AC XY: 3AN XY: 212640
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GnomAD4 genome AF: 0.00000678 AC: 1AN: 147502Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 71586
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at