rs587777291
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4_SupportingPP5
The NM_173086.5(KRT6C):c.516_518del(p.Asn172del) variant causes a inframe deletion change. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 20)
Consequence
KRT6C
NM_173086.5 inframe_deletion
NM_173086.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.49
Genes affected
KRT6C (HGNC:20406): (keratin 6C) Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. The type II keratins are clustered in a region of chromosome 12q13. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_173086.5. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 12-52473219-CTTG-C is Pathogenic according to our data. Variant chr12-52473219-CTTG-C is described in ClinVar as [Pathogenic]. Clinvar id is 126525.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr12-52473219-CTTG-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT6C | NM_173086.5 | c.516_518del | p.Asn172del | inframe_deletion | 1/9 | ENST00000252250.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT6C | ENST00000252250.7 | c.516_518del | p.Asn172del | inframe_deletion | 1/9 | 1 | NM_173086.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 20
GnomAD3 genomes
?
Cov.:
20
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 20
GnomAD4 genome
?
Cov.:
20
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Focal palmoplantar keratoderma Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2010 | - - |
not provided Other:1
not provided, no classification provided | literature only | Epithelial Biology; Institute of Medical Biology, Singapore | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at