rs1085307096
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Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM4PP3PP5_Moderate
The NM_005630.3(SLCO2A1):βc.1279_1290delβ(p.Glu427_Pro430del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,730 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely pathogenic (β ).
Frequency
Genomes: π 0.000013 ( 0 hom., cov: 32)
Exomes π: 0.000038 ( 1 hom. )
Consequence
SLCO2A1
NM_005630.3 inframe_deletion
NM_005630.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.25
Genes affected
SLCO2A1 (HGNC:10955): (solute carrier organic anion transporter family member 2A1) This gene encodes a prostaglandin transporter that is a member of the 12-membrane-spanning superfamily of transporters. The encoded protein may be involved in mediating the uptake and clearance of prostaglandins in numerous tissues. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_005630.3.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 3-133947260-GGGGGTAGACTTC-G is Pathogenic according to our data. Variant chr3-133947260-GGGGGTAGACTTC-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 225479.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO2A1 | NM_005630.3 | c.1279_1290del | p.Glu427_Pro430del | inframe_deletion | 9/14 | ENST00000310926.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO2A1 | ENST00000310926.11 | c.1279_1290del | p.Glu427_Pro430del | inframe_deletion | 9/14 | 1 | NM_005630.3 | P1 | |
SLCO2A1 | ENST00000493729.5 | c.1051_1062del | p.Glu351_Pro354del | inframe_deletion | 8/13 | 5 | |||
SLCO2A1 | ENST00000462770.5 | n.859_870del | non_coding_transcript_exon_variant | 5/7 | 2 | ||||
SLCO2A1 | ENST00000481359.3 | c.1105+1264_1105+1275del | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250968Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135672
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GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461564Hom.: 1 AF XY: 0.0000316 AC XY: 23AN XY: 727120
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypertrophic osteoarthropathy, primary, autosomal recessive, 2 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | reference population | Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center | Mar 18, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at