KRTAP1-1

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

Basic information

Region (hg38): 17:41040540-41041450

Links

ENSG00000188581 ∙ NCBI:81851 ∙ OMIM:608819 ∙ HGNC:16772 ∙ Uniprot:Q07627 ∙ 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 KRTAP1-1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP1-1 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						0
missense			16	2		18
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	1

Variants in KRTAP1-1

This is a list of pathogenic ClinVar variants found in the KRTAP1-1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-41040905-G-A		not specified	Uncertain significance (Mar 14, 2023)
17-41040941-A-G		not specified	Uncertain significance (Mar 07, 2023)
17-41040950-C-T		not specified	Uncertain significance (Apr 05, 2023)
17-41040976-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-41040995-C-G		not specified	Uncertain significance (Jun 24, 2022)
17-41041016-T-C		not specified	Uncertain significance (Oct 20, 2021)
17-41041028-G-A		not specified	Uncertain significance (Dec 03, 2021)
17-41041030-C-G		not specified	Uncertain significance (Jun 17, 2024)
17-41041039-C-A		not specified	Uncertain significance (Sep 16, 2021)
17-41041040-G-A		not specified	Uncertain significance (Jan 10, 2023)
17-41041048-C-T		not specified	Uncertain significance (Apr 04, 2024)
17-41041052-T-C		not specified	Likely benign (Jan 26, 2022)
17-41041094-C-T		not specified	Uncertain significance (Jan 18, 2023)
17-41041096-A-G		not specified	Uncertain significance (Dec 21, 2023)
17-41041147-C-G		not specified	Likely benign (Jul 16, 2021)
17-41041162-C-T		not specified	Uncertain significance (Mar 30, 2024)
17-41041174-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-41041188-GC-G		not specified	Benign (Jun 25, 2015)
17-41041213-G-T		not specified	Uncertain significance (Nov 05, 2021)
17-41041314-G-T		not specified	Uncertain significance (Mar 27, 2023)
17-41041342-G-T		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTAP1-1	protein_coding	protein_coding	ENST00000306271	1	903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000597	0.152	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0425	105	104	1.01	0.00000606	1153
Missense in Polyphen		38	40.234	0.94448		367
Synonymous	-0.962	45	37.5	1.20	0.00000209	324
Loss of Function	-0.686	7	5.30	1.32	2.33e-7	64

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: 0.800
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.99

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.226

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krtap1-5

Gene ontology

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