KRTAP10-1

keratin associated protein 10-1, the group of Keratin associated proteins

Basic information

Region (hg38): 21:44538981-44540195

Previous symbols: [ "KRTAP18-1" ]

Links

ENSG00000215455 ∙ NCBI:386677 ∙ ∙ HGNC:22966 ∙ Uniprot:P60331 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRTAP10-1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP10-1 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				1		1
missense			29	5	4	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	6	4

Variants in KRTAP10-1

This is a list of pathogenic ClinVar variants found in the KRTAP10-1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-44539309-G-T		not specified	Uncertain significance (Feb 07, 2023)
21-44539314-G-A			Likely benign (May 01, 2022)
21-44539322-A-T		not specified	Uncertain significance (Jan 03, 2024)
21-44539325-C-T		not specified	Likely benign (Apr 19, 2023)
21-44539330-C-T		not specified	Uncertain significance (Nov 29, 2023)
21-44539331-G-A		not specified	Uncertain significance (Jun 13, 2024)
21-44539333-C-G		not specified	Uncertain significance (Mar 30, 2022)
21-44539373-C-A		Autosomal recessive nonsyndromic hearing loss 98	Uncertain significance (May 08, 2018)
21-44539373-C-G			Benign (Oct 01, 2023)
21-44539382-A-T		not specified	Uncertain significance (Mar 07, 2023)
21-44539388-C-T		not specified	Likely benign (May 11, 2022)
21-44539393-G-T		not specified	Uncertain significance (Aug 17, 2021)
21-44539397-A-G			Benign (Feb 01, 2024)
21-44539408-A-T		not specified	Uncertain significance (Jun 29, 2023)
21-44539414-A-T		not specified	Uncertain significance (Jun 17, 2024)
21-44539417-C-T		not specified	Uncertain significance (Dec 14, 2023)
21-44539447-A-G		not specified	Uncertain significance (Dec 28, 2023)
21-44539466-A-G		not specified	Uncertain significance (Dec 27, 2023)
21-44539508-T-C		not specified	Uncertain significance (Jan 03, 2024)
21-44539538-C-T		not specified	Uncertain significance (Oct 19, 2021)
21-44539547-C-T		not specified	Uncertain significance (Mar 18, 2024)
21-44539577-C-T		not specified	Uncertain significance (Jun 07, 2023)
21-44539600-C-T		not specified	Likely benign (Aug 09, 2021)
21-44539607-C-A		not specified	Uncertain significance (Aug 09, 2021)
21-44539630-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTAP10-1	protein_coding	protein_coding	ENST00000400375	1	1215

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000168	0.465	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.39	212	162	1.31	0.0000102	1789
Missense in Polyphen		0	0.24584	0		2
Synonymous	-4.43	119	71.4	1.67	0.00000507	564
Loss of Function	0.287	6	6.81	0.881	3.08e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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.

Intolerance Scores

• loftool: 0.664
• rvis_EVS: 2.78
• rvis_percentile_EVS: 99.02

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.112
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: keratinization
• Cellular component: cytosol;keratin filament