12-52519137-G-C

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PS1PM1PM2PP3_StrongPP5_Moderate

The NM_000424.4(KRT5):​c.579C>G​(p.Asn193Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Pathogenic in Lovd.

Frequency

Genomes: not found (cov: 33)

Consequence

KRT5
NM_000424.4 missense

Scores

13
4
2

Clinical Significance

Pathogenic criteria provided, single submitter P:2O:1

Conservation

PhyloP100: 4.94
Variant links:
Genes affected
KRT5 (HGNC:6442): (keratin 5) The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. This type II cytokeratin is specifically expressed in the basal layer of the epidermis with family member KRT14. Mutations in these genes have been associated with a complex of diseases termed epidermolysis bullosa simplex. The type II cytokeratins are clustered in a region of chromosome 12q12-q13. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PS1
Transcript NM_000424.4 (KRT5) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in Lovd
PM1
In a region_of_interest Coil 1A (size 35) in uniprot entity K2C5_HUMAN there are 13 pathogenic changes around while only 0 benign (100%) in NM_000424.4
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.983
PP5
Variant 12-52519137-G-C is Pathogenic according to our data. Variant chr12-52519137-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 14644.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KRT5NM_000424.4 linkc.579C>G p.Asn193Lys missense_variant 2/9 ENST00000252242.9 NP_000415.2 P13647

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KRT5ENST00000252242.9 linkc.579C>G p.Asn193Lys missense_variant 2/91 NM_000424.4 ENSP00000252242.4 P13647

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
38
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:2Other:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Epidermolysis bullosa simplex 2C, localized Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMJan 01, 1996- -
Epidermolysis bullosa simplex Pathogenic:1
Pathogenic, criteria provided, single submitterresearchBiomedical Innovation Departament, CIEMATNov 12, 2014- -
not provided Other:1
not provided, no classification providedliterature onlyEpithelial Biology; Institute of Medical Biology, Singapore-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
BayesDel_addAF
Pathogenic
0.26
D
BayesDel_noAF
Uncertain
0.13
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.94
D;D
Eigen
Pathogenic
1.0
Eigen_PC
Pathogenic
0.87
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.79
T;T
M_CAP
Uncertain
0.11
D
MetaRNN
Pathogenic
0.98
D;D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Pathogenic
4.2
H;.
PrimateAI
Pathogenic
0.80
D
PROVEAN
Pathogenic
-5.2
D;D
REVEL
Pathogenic
0.76
Sift
Pathogenic
0.0
D;D
Sift4G
Pathogenic
0.0010
D;.
Polyphen
1.0
D;.
Vest4
0.98
MutPred
0.95
Gain of MoRF binding (P = 0.041);.;
MVP
0.99
MPC
0.89
ClinPred
1.0
D
GERP RS
4.3
Varity_R
0.89
gMVP
0.97

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs60586163; hg19: chr12-52912921; API