rs1554293083
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001031710.3(KLHL7):c.1291del(p.Leu431Ter) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
KLHL7
NM_001031710.3 frameshift
NM_001031710.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0280
Genes affected
KLHL7 (HGNC:15646): (kelch like family member 7) This gene encodes a BTB-Kelch-related protein. The encoded protein may be involved in protein degradation. Mutations in this gene have been associated with retinitis pigmentosa 42. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 7-23167947-GC-G is Pathogenic according to our data. Variant chr7-23167947-GC-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 487515.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL7 | NM_001031710.3 | c.1291del | p.Leu431Ter | frameshift_variant | 9/11 | ENST00000339077.10 | |
KLHL7 | NM_018846.5 | c.1147del | p.Leu383Ter | frameshift_variant | 9/11 | ||
KLHL7 | NR_033328.2 | n.1664del | non_coding_transcript_exon_variant | 10/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL7 | ENST00000339077.10 | c.1291del | p.Leu431Ter | frameshift_variant | 9/11 | 1 | NM_001031710.3 | P1 | |
KLHL7 | ENST00000409689.5 | c.1147del | p.Leu383Ter | frameshift_variant | 9/11 | 1 | |||
KLHL7 | ENST00000521082.5 | c.*1299del | 3_prime_UTR_variant, NMD_transcript_variant | 10/12 | 1 | ||||
KLHL7 | ENST00000469576.1 | n.178del | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Ulnar deviation of the wrist Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | Nov 01, 2016 | - - |
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