rs377327186
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182507.3(KRT80):c.1082G>T(p.Arg361Leu) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Consequence
KRT80
NM_182507.3 missense
NM_182507.3 missense
Scores
1
3
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0140
Genes affected
KRT80 (HGNC:27056): (keratin 80) Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. This gene's expression profile shows that it encodes a type II epithelial keratin, although structurally the encoded protein is more like a type II hair keratin. This protein is involved in cell differentiation, localizing near desmosomal plaques in earlier stages of differentiation but then dispersing throughout the cytoplasm in terminally differentiating cells. The type II keratins are clustered in a region of chromosome 12q13. Two transcript variants encoding two different fully functional isoforms have been found for this gene.[provided by RefSeq, Oct 2010]
Genome browser will be placed here
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=0.16789272).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| KRT80 | NM_182507.3 | c.1082G>T | p.Arg361Leu | missense_variant | Exon 7 of 9 | ENST00000394815.3 | NP_872313.2 | |
| KRT80 | NM_001081492.2 | c.1082G>T | p.Arg361Leu | missense_variant | Exon 7 of 9 | NP_001074961.1 | ||
| KRT80 | XM_005268676.4 | c.1187G>T | p.Arg396Leu | missense_variant | Exon 5 of 7 | XP_005268733.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| KRT80 | ENST00000394815.3 | c.1082G>T | p.Arg361Leu | missense_variant | Exon 7 of 9 | 1 | NM_182507.3 | ENSP00000378292.2 | ||
| KRT80 | ENST00000313234.9 | c.1082G>T | p.Arg361Leu | missense_variant | Exon 7 of 9 | 1 | ENSP00000369361.2 | |||
| KRT80 | ENST00000466011.1 | n.1238G>T | non_coding_transcript_exon_variant | Exon 5 of 7 | 2 | |||||
| LINC00592 | ENST00000640420.1 | n.413+7343C>A | intron_variant | Intron 2 of 2 | 5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Uncertain
.;D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
T;T
Polyphen
B;B
Vest4
MutPred
Loss of MoRF binding (P = 0.0061);Loss of MoRF binding (P = 0.0061);
MVP
MPC
0.14
ClinPred
T
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