5-137618759-CAAAA-CAAAAAA
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017415.3(KLHL3):c.*3337_*3338dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000181 in 110,640 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 0.000018 ( 0 hom., cov: 22)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KLHL3
NM_017415.3 3_prime_UTR
NM_017415.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.572
Genes affected
KLHL3 (HGNC:6354): (kelch like family member 3) This gene is ubiquitously expressed and encodes a full-length protein which has an N-terminal BTB domain followed by a BACK domain and six kelch-like repeats in the C-terminus. These kelch-like repeats promote substrate ubiquitination of bound proteins via interaction of the BTB domain with the CUL3 (cullin 3) component of a cullin-RING E3 ubiquitin ligase (CRL) complex. Muatations in this gene cause pseudohypoaldosteronism type IID (PHA2D); a rare Mendelian syndrome featuring hypertension, hyperkalaemia and metabolic acidosis. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Mar 2012]
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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
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLHL3 | NM_017415.3 | c.*3337_*3338dupTT | 3_prime_UTR_variant | Exon 15 of 15 | ENST00000309755.9 | NP_059111.2 | ||
KLHL3 | NM_001257194.1 | c.*3337_*3338dupTT | 3_prime_UTR_variant | Exon 15 of 15 | NP_001244123.1 | |||
KLHL3 | NM_001257195.2 | c.*3337_*3338dupTT | 3_prime_UTR_variant | Exon 13 of 13 | NP_001244124.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLHL3 | ENST00000309755 | c.*3337_*3338dupTT | 3_prime_UTR_variant | Exon 15 of 15 | 1 | NM_017415.3 | ENSP00000312397.4 | |||
KLHL3 | ENST00000508657 | c.*3337_*3338dupTT | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000422099.1 | ||||
KLHL3 | ENST00000506491 | c.*3337_*3338dupTT | 3_prime_UTR_variant | Exon 13 of 13 | 1 | ENSP00000424828.1 | ||||
KLHL3 | ENST00000509694.1 | n.623-897_623-896dupTT | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000181 AC: 2AN: 110600Hom.: 0 Cov.: 22
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 6Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 6
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GnomAD4 genome AF: 0.0000181 AC: 2AN: 110640Hom.: 0 Cov.: 22 AF XY: 0.0000377 AC XY: 2AN XY: 53060
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at