rs1057524882
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003597.5(KLF11):c.608_609delinsAG(p.Gly203Glu) variant causes a missense 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 Uncertain significance (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Genomes: not found (cov: 33)
Consequence
KLF11
NM_003597.5 missense
NM_003597.5 missense
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.224
Genes affected
KLF11 (HGNC:11811): (KLF transcription factor 11) The protein encoded by this gene is a zinc finger transcription factor that binds to SP1-like sequences in epsilon- and gamma-globin gene promoters. This binding inhibits cell growth and causes apoptosis. Defects in this gene are a cause of maturity-onset diabetes of the young type 7 (MODY7). Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]
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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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF11 | NM_003597.5 | c.608_609delinsAG | p.Gly203Glu | missense_variant | 3/4 | ENST00000305883.6 | |
KLF11 | NM_001177716.2 | c.557_558delinsAG | p.Gly186Glu | missense_variant | 3/4 | ||
KLF11 | NM_001177718.2 | c.557_558delinsAG | p.Gly186Glu | missense_variant | 3/4 | ||
KLF11 | XM_047446025.1 | c.557_558delinsAG | p.Gly186Glu | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF11 | ENST00000305883.6 | c.608_609delinsAG | p.Gly203Glu | missense_variant | 3/4 | 1 | NM_003597.5 | A2 | |
KLF11 | ENST00000535335.1 | c.557_558delinsAG | p.Gly186Glu | missense_variant | 3/4 | 2 | P4 | ||
KLF11 | ENST00000540845.5 | c.557_558delinsAG | p.Gly186Glu | missense_variant | 3/4 | 2 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Monogenic diabetes Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | Apr 08, 2016 | ACMG Criteria: PM2, PP3, BP4 - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2022 | Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 393367). This variant has not been reported in the literature in individuals affected with KLF11-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.3%). This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 203 of the KLF11 protein (p.Gly203Glu). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at