KRTAP10-4

keratin associated protein 10-4, the group of Keratin associated proteins

Basic information

Region (hg38): 21:44573729-44575371

Previous symbols: [ "KRTAP18-4" ]

Links

ENSG00000215454NCBI:386672HGNC:20521Uniprot:P60372AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRTAP10-4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP10-4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
5
clinvar
5
missense
28
clinvar
3
clinvar
1
clinvar
32
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 28 8 1

Variants in KRTAP10-4

This is a list of pathogenic ClinVar variants found in the KRTAP10-4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
21-44573796-G-A not specified Uncertain significance (Aug 02, 2021)2366698
21-44573804-C-T not specified Uncertain significance (Jul 19, 2023)2594076
21-44573816-T-C not specified Uncertain significance (Jan 23, 2023)2477190
21-44573877-C-A not specified Uncertain significance (Jan 02, 2024)3116861
21-44573900-G-A not specified Uncertain significance (Dec 01, 2022)2363882
21-44573913-G-C not specified Uncertain significance (Jul 14, 2021)2374772
21-44573947-G-A Likely benign (Jun 01, 2023)2652763
21-44573955-C-T not specified Uncertain significance (Dec 12, 2023)3116862
21-44574027-G-T not specified Uncertain significance (May 30, 2024)3289623
21-44574048-T-C not specified Likely benign (Nov 01, 2022)2352184
21-44574058-T-C Likely benign (Jul 01, 2024)3250692
21-44574059-G-A not specified Likely benign (Dec 17, 2023)3116863
21-44574068-C-T not specified Uncertain significance (Jun 22, 2023)2592359
21-44574088-C-T Likely benign (Jan 01, 2023)1695031
21-44574089-G-A not specified Uncertain significance (Jun 24, 2022)2363835
21-44574093-C-A not specified Uncertain significance (Oct 10, 2023)3116864
21-44574113-T-C Benign (Jul 22, 2016)377329
21-44574153-A-C not specified Likely benign (Jun 04, 2024)3289624
21-44574225-G-A not specified Uncertain significance (Dec 12, 2023)3116865
21-44574226-T-G not specified Uncertain significance (Apr 04, 2024)3289619
21-44574270-C-T not specified Likely benign (Feb 27, 2023)2455557
21-44574326-G-A not specified Uncertain significance (Apr 07, 2022)2398497
21-44574331-T-C Likely benign (Aug 01, 2022)2652764
21-44574359-A-T not specified Uncertain significance (Feb 03, 2022)2275280
21-44574373-G-A Likely benign (Sep 01, 2022)2652765

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KRTAP10-4protein_codingprotein_codingENST00000400374 11382
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.19e-130.010300000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.382792211.260.00001272553
Missense in Polyphen3325.0681.3164292
Synonymous-0.38410297.21.050.00000643776
Loss of Function-0.6521714.31.196.36e-7169

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high- sulfur and high-glycine-tyrosine keratins.;
Pathway
Vitamin D Receptor Pathway (Consensus)

Recessive Scores

pRec
0.0922

Intolerance Scores

loftool
0.875
rvis_EVS
2.47
rvis_percentile_EVS
98.61

Haploinsufficiency Scores

pHI
0.107
hipred
N
hipred_score
0.187
ghis
0.394

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.167

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh

Gene ontology

Biological process
keratinization
Cellular component
cytosol;keratin filament
Molecular function
protein binding