rs532875586

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000224.3(KRT18):​c.206G>A​(p.Gly69Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 40)
Failed GnomAD Quality Control

Consequence

KRT18
NM_000224.3 missense

Scores

1
6
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.355
Variant links:
Genes affected
KRT18 (HGNC:6430): (keratin 18) KRT18 encodes the type I intermediate filament chain keratin 18. Keratin 18, together with its filament partner keratin 8, are perhaps the most commonly found members of the intermediate filament gene family. They are expressed in single layer epithelial tissues of the body. Mutations in this gene have been linked to cryptogenic cirrhosis. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
KRT8 (HGNC:6446): (keratin 8) This gene is a member of the type II keratin family clustered on the long arm of chromosome 12. Type I and type II keratins heteropolymerize to form intermediate-sized filaments in the cytoplasm of epithelial cells. The product of this gene typically dimerizes with keratin 18 to form an intermediate filament in simple single-layered epithelial cells. This protein plays a role in maintaining cellular structural integrity and also functions in signal transduction and cellular differentiation. Mutations in this gene cause cryptogenic cirrhosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.20551115).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KRT18NM_000224.3 linkc.206G>A p.Gly69Glu missense_variant Exon 1 of 7 ENST00000388835.4 NP_000215.1 P05783A0A024RAY2
KRT18NM_199187.2 linkc.206G>A p.Gly69Glu missense_variant Exon 2 of 8 NP_954657.1 P05783A0A024RAY2
KRT8NM_001256293.2 linkc.-47+336C>T intron_variant Intron 1 of 8 NP_001243222.1 P05787-1
KRT8NR_045962.2 linkn.405+77C>T intron_variant Intron 1 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRT18ENST00000388835.4 linkc.206G>A p.Gly69Glu missense_variant Exon 1 of 7 1 NM_000224.3 ENSP00000373487.3 P05783

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151856
Hom.:
0
Cov.:
40
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
36
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
151856
Hom.:
0
Cov.:
40
AF XY:
0.00
AC XY:
0
AN XY:
74182
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Pathogenic
0.18
D
BayesDel_noAF
Uncertain
0.020
CADD
Benign
22
DANN
Benign
0.88
DEOGEN2
Benign
0.23
T;.;T
Eigen
Benign
-0.24
Eigen_PC
Benign
-0.19
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Benign
0.77
T;T;.
M_CAP
Uncertain
0.088
D
MetaRNN
Benign
0.21
T;T;T
MetaSVM
Uncertain
-0.20
T
MutationAssessor
Benign
1.9
L;.;L
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-1.7
N;N;N
REVEL
Uncertain
0.56
Sift
Benign
0.23
T;T;T
Sift4G
Benign
0.083
T;D;T
Polyphen
0.0040
B;B;B
Vest4
0.34
MutPred
0.44
Gain of catalytic residue at L71 (P = 0);Gain of catalytic residue at L71 (P = 0);Gain of catalytic residue at L71 (P = 0);
MVP
0.95
MPC
0.69
ClinPred
0.13
T
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.15
gMVP
0.63

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: rs532875586; hg19: chr12-53343163; API