rs371683842

Variant summary

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

The NM_002281.4(KRT81):ā€‹c.1324G>Cā€‹(p.Val442Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000714 in 1,400,486 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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)
Exomes š‘“: 7.1e-7 ( 0 hom. )

Consequence

KRT81
NM_002281.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.170
Variant links:
Genes affected
KRT81 (HGNC:6458): (keratin 81) The protein encoded by this gene is a member of the keratin gene family. As a type II hair keratin, it is a basic protein which heterodimerizes with type I keratins to form hair and nails. The type II hair keratins are clustered in a region of chromosome 12q13 and are grouped into two distinct subfamilies based on structure similarity. One subfamily, consisting of KRTHB1, KRTHB3, and KRTHB6, is highly related. The other less-related subfamily includes KRTHB2, KRTHB4, and KRTHB5. All hair keratins are expressed in the hair follicle; this hair keratin, as well as KRTHB3 and KRTHB6, is found primarily in the hair cortex. Mutations in this gene and KRTHB6 have been observed in patients with a rare dominant hair disease, monilethrix. Some human genome assemblies (example T2T-CHM13) have a non-coding version of the gene due to the presence of a SNP that introduces a premature stop codon after codon 281. [provided by RefSeq, Jan 2024]
KRT86 (HGNC:6463): (keratin 86) This gene encodes a type II keratin protein, which heterodimerizes with type I keratins to form hair and nails. This gene is present in a cluster of related genes and pseudogenes on chromosome 12. Mutations in this gene have been observed in patients with the hair disease monilethrix. [provided by RefSeq, Feb 2016]

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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=0.078755885).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KRT81NM_002281.4 linkc.1324G>C p.Val442Leu missense_variant Exon 9 of 9 ENST00000327741.9 NP_002272.2 Q14533
KRT86NM_001320198.2 linkc.-5+10503C>G intron_variant Intron 2 of 10 ENST00000423955.7 NP_001307127.1 O43790A8K872
KRT86XM_005268866.5 linkc.129+10503C>G intron_variant Intron 2 of 10 XP_005268923.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRT81ENST00000327741.9 linkc.1324G>C p.Val442Leu missense_variant Exon 9 of 9 1 NM_002281.4 ENSP00000369349.4 Q14533
KRT86ENST00000423955.7 linkc.-5+10503C>G intron_variant Intron 2 of 10 2 NM_001320198.2 ENSP00000444533.1 O43790
KRT86ENST00000553310.6 linkc.-4-15464C>G intron_variant Intron 1 of 2 4 ENSP00000452237.3 U3KPR1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.14e-7
AC:
1
AN:
1400486
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
690970
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.26e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.092
T
BayesDel_noAF
Benign
-0.37
CADD
Benign
11
DANN
Benign
0.97
DEOGEN2
Benign
0.040
T;.
Eigen
Benign
-0.68
Eigen_PC
Benign
-0.61
FATHMM_MKL
Benign
0.13
N
LIST_S2
Benign
0.11
T;T
M_CAP
Benign
0.057
D
MetaRNN
Benign
0.079
T;T
MetaSVM
Benign
-0.84
T
MutationAssessor
Benign
1.4
L;.
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-0.83
N;.
REVEL
Benign
0.19
Sift
Benign
0.21
T;.
Sift4G
Benign
0.79
T;T
Polyphen
0.0010
B;.
Vest4
0.21
MutPred
0.43
Gain of catalytic residue at V442 (P = 0);Gain of catalytic residue at V442 (P = 0);
MVP
0.22
MPC
0.37
ClinPred
0.096
T
GERP RS
2.5
Varity_R
0.096
gMVP
0.043

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs371683842; hg19: chr12-52680233; API