GeneBe

rs754896740

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_031958.2(KRTAP3-1):​c.265G>T​(p.Gly89Cys) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G89S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

KRTAP3-1
NM_031958.2 missense

Scores

16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.172

Publications

0 publications found
Variant links:
Genes affected
KRTAP3-1 (HGNC:16778): (keratin associated protein 3-1) This protein is a member of the keratin-associated protein (KAP) family. The KAP proteins form a matrix of keratin intermediate filaments which contribute to the structure of hair fibers. KAP family members appear to have unique, family-specific amino- and carboxyl-terminal regions and are subdivided into three multi-gene families according to amino acid composition: the high sulfur, the ultrahigh sulfur, and the high tyrosine/glycine KAPs. This protein is a member of the high sulfur KAP family and the gene is localized to a cluster of KAPs at 17q12-q21. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.07435447).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031958.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KRTAP3-1
NM_031958.2
MANE Select
c.265G>Tp.Gly89Cys
missense
Exon 1 of 1NP_114164.1Q9BYR8

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KRTAP3-1
ENST00000391588.3
TSL:6 MANE Select
c.265G>Tp.Gly89Cys
missense
Exon 1 of 1ENSP00000375430.1Q9BYR8
KRTAP3-1
ENST00000581033.1
TSL:3
n.367G>T
non_coding_transcript_exon
Exon 3 of 3
ENSG00000306126
ENST00000815517.1
n.219+28203C>A
intron
N/A

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00000401
AC:
1
AN:
249378
AF XY:
0.00000742
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000888
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
6.8
DANN
Benign
0.84
DEOGEN2
Benign
0.0032
T
Eigen
Benign
-0.71
Eigen_PC
Benign
-0.64
FATHMM_MKL
Benign
0.085
N
M_CAP
Benign
0.0042
T
MetaRNN
Benign
0.074
T
MetaSVM
Benign
-1.0
T
PhyloP100
-0.17
PrimateAI
Benign
0.32
T
PROVEAN
Benign
1.3
N
REVEL
Benign
0.018
Sift
Benign
0.26
T
Sift4G
Benign
0.12
T
Polyphen
0.015
B
Vest4
0.30
MutPred
0.42
Loss of sheet (P = 0.0817)
MVP
0.14
MPC
0.017
ClinPred
0.11
T
GERP RS
0.69
PromoterAI
-0.0034
Neutral
Varity_R
0.074
gMVP
0.13

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs754896740; hg19: chr17-39165062; API