rs121909143
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1PM2PP5BP4
The NM_001300.6(KLF6):c.506T>C(p.Leu169Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
KLF6
NM_001300.6 missense
NM_001300.6 missense
Scores
1
4
14
Clinical Significance
Conservation
PhyloP100: 4.42
Genes affected
KLF6 (HGNC:2235): (KLF transcription factor 6) This gene encodes a member of the Kruppel-like family of transcription factors. The zinc finger protein is a transcriptional activator, and functions as a tumor suppressor. Multiple transcript variants encoding different isoforms have been found for this gene, some of which are implicated in carcinogenesis. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM1
?
In a chain Krueppel-like factor 6 (size 282) in uniprot entity KLF6_HUMAN there are 5 pathogenic changes around while only 2 benign (71%) in NM_001300.6
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 10-3781811-A-G is Pathogenic according to our data. Variant chr10-3781811-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 7573.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.19615185). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF6 | NM_001300.6 | c.506T>C | p.Leu169Pro | missense_variant | 2/4 | ENST00000497571.6 | |
KLF6 | NM_001160124.2 | c.506T>C | p.Leu169Pro | missense_variant | 2/4 | ||
KLF6 | NM_001160125.2 | c.506T>C | p.Leu169Pro | missense_variant | 2/3 | ||
KLF6 | NR_027653.2 | n.701T>C | non_coding_transcript_exon_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF6 | ENST00000497571.6 | c.506T>C | p.Leu169Pro | missense_variant | 2/4 | 1 | NM_001300.6 | 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:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Prostate cancer, somatic Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 21, 2001 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Uncertain
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
T;D;D
Polyphen
B;.;B
Vest4
MutPred
Gain of glycosylation at L169 (P = 0.0095);Gain of glycosylation at L169 (P = 0.0095);Gain of glycosylation at L169 (P = 0.0095);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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