rs1135402746
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP5BS2
The NM_001365677.2(P4HA2):c.1352_1353del(p.Val451GlyfsTer9) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
P4HA2
NM_001365677.2 frameshift
NM_001365677.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.95
Genes affected
P4HA2 (HGNC:8547): (prolyl 4-hydroxylase subunit alpha 2) This gene encodes a component of prolyl 4-hydroxylase, a key enzyme in collagen synthesis composed of two identical alpha subunits and two beta subunits. The encoded protein is one of several different types of alpha subunits and provides the major part of the catalytic site of the active enzyme. In collagen and related proteins, prolyl 4-hydroxylase catalyzes the formation of 4-hydroxyproline that is essential to the proper three-dimensional folding of newly synthesized procollagen chains. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 5-132198223-CCA-C is Pathogenic according to our data. Variant chr5-132198223-CCA-C is described in ClinVar as [Pathogenic]. Clinvar id is 372167.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
?
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P4HA2 | NM_001365677.2 | c.1352_1353del | p.Val451GlyfsTer9 | frameshift_variant | 12/15 | ENST00000379104.7 | |
P4HA2 | NM_001017974.2 | c.1365+96_1365+97del | intron_variant | ENST00000360568.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P4HA2 | ENST00000379104.7 | c.1352_1353del | p.Val451GlyfsTer9 | frameshift_variant | 12/15 | 1 | NM_001365677.2 | P4 | |
P4HA2 | ENST00000360568.8 | c.1365+96_1365+97del | intron_variant | 1 | NM_001017974.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251434Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135888
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461868Hom.: 0 AF XY: 0.00000413 AC XY: 3AN XY: 727238
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Myopia 25, autosomal dominant Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 05, 2016 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at