KRTAP10-4

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

Basic information

Region (hg38): 21:44573728-44575371

Previous symbols: [ "KRTAP18-4" ]

Links

ENSG00000215454 ∙ NCBI:386672 ∙ ∙ HGNC:20521 ∙ Uniprot:P60372 ∙ 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 KRTAP10-4 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		5
missense			28	3	1	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)
21-44573804-C-T		not specified	Uncertain significance (Jul 19, 2023)
21-44573816-T-C		not specified	Uncertain significance (Jan 23, 2023)
21-44573877-C-A		not specified	Uncertain significance (Jan 02, 2024)
21-44573900-G-A		not specified	Uncertain significance (Dec 01, 2022)
21-44573913-G-C		not specified	Uncertain significance (Jul 14, 2021)
21-44573947-G-A			Likely benign (Jun 01, 2023)
21-44573955-C-T		not specified	Uncertain significance (Dec 12, 2023)
21-44574027-G-T		not specified	Uncertain significance (May 30, 2024)
21-44574048-T-C		not specified	Likely benign (Nov 01, 2022)
21-44574058-T-C			Likely benign (Jul 01, 2024)
21-44574059-G-A		not specified	Likely benign (Dec 17, 2023)
21-44574068-C-T		not specified	Uncertain significance (Jun 22, 2023)
21-44574088-C-T			Likely benign (Jan 01, 2023)
21-44574089-G-A		not specified	Uncertain significance (Jun 24, 2022)
21-44574093-C-A		not specified	Uncertain significance (Oct 10, 2023)
21-44574113-T-C			Benign (Jul 22, 2016)
21-44574153-A-C		not specified	Likely benign (Jun 04, 2024)
21-44574225-G-A		not specified	Uncertain significance (Dec 12, 2023)
21-44574226-T-G		not specified	Uncertain significance (Apr 04, 2024)
21-44574270-C-T		not specified	Likely benign (Feb 27, 2023)
21-44574326-G-A		not specified	Uncertain significance (Apr 07, 2022)
21-44574331-T-C			Likely benign (Aug 01, 2022)
21-44574359-A-T		not specified	Uncertain significance (Feb 03, 2022)
21-44574373-G-A			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTAP10-4	protein_coding	protein_coding	ENST00000400374	1	1382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.19e-13	0.0103	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.38	279	221	1.26	0.0000127	2553
Missense in Polyphen		33	25.068	1.3164		292
Synonymous	-0.384	102	97.2	1.05	0.00000643	776
Loss of Function	-0.652	17	14.3	1.19	6.36e-7	169

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.
• 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

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

Gene ontology

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