rs267606580
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The ENST00000279146.8(AIP):c.824dup(p.His275GlnfsTer13) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. H275H) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Consequence
AIP
ENST00000279146.8 frameshift
ENST00000279146.8 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.09
Genes affected
AIP (HGNC:358): (aryl hydrocarbon receptor interacting protein) The protein encoded by this gene is a receptor for aryl hydrocarbons and a ligand-activated transcription factor. The encoded protein is found in the cytoplasm as part of a multiprotein complex, but upon binding of ligand is transported to the nucleus. This protein can regulate the expression of many xenobiotic metabolizing enzymes. Also, the encoded protein can bind specifically to and inhibit the activity of hepatitis B virus. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 6 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 11-67490823-C-CA is Pathogenic according to our data. Variant chr11-67490823-C-CA is described in ClinVar as [Pathogenic]. Clinvar id is 4890.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AIP | NM_003977.4 | c.824dup | p.His275GlnfsTer13 | frameshift_variant | 6/6 | ENST00000279146.8 | NP_003968.3 | |
AIP | NM_001302959.2 | c.647dup | p.His216GlnfsTer13 | frameshift_variant | 6/6 | NP_001289888.1 | ||
AIP | NM_001302960.2 | c.816dup | p.Arg273ThrfsTer28 | frameshift_variant | 6/6 | NP_001289889.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AIP | ENST00000279146.8 | c.824dup | p.His275GlnfsTer13 | frameshift_variant | 6/6 | 1 | NM_003977.4 | ENSP00000279146 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Somatotroph adenoma Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 06, 2007 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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