KRTAP4-4

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

Basic information

Region (hg38): 17:41159649-41160748

Previous symbols: [ "KRTAP4-13" ]

Links

ENSG00000171396 ∙ NCBI:84616 ∙ ∙ HGNC:16928 ∙ Uniprot:Q9BYR3 ∙ 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 KRTAP4-4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP4-4 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				4		4
missense			18	1	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	5	1

Variants in KRTAP4-4

This is a list of pathogenic ClinVar variants found in the KRTAP4-4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-41160295-G-T		not specified	Uncertain significance (Jun 29, 2022)
17-41160340-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-41160370-G-T		not specified	Uncertain significance (May 24, 2024)
17-41160387-C-A		not specified	Uncertain significance (Nov 10, 2024)
17-41160401-C-T			Likely benign (Feb 01, 2023)
17-41160404-A-G			Likely benign (Feb 01, 2023)
17-41160406-A-G		not specified	Uncertain significance (Apr 11, 2023)
17-41160413-A-G			Likely benign (Feb 01, 2023)
17-41160425-T-C			Likely benign (Feb 01, 2023)
17-41160449-G-C		not specified	Uncertain significance (May 04, 2023)
17-41160480-C-A		not specified	Uncertain significance (Aug 26, 2024)
17-41160495-C-T		not specified	Uncertain significance (Sep 04, 2024)
17-41160520-T-A		not specified	Uncertain significance (Jun 29, 2023)
17-41160550-G-A		not specified	Uncertain significance (Nov 24, 2024)
17-41160561-C-G		not specified	Uncertain significance (Mar 27, 2023)
17-41160573-C-A		not specified	Uncertain significance (Mar 28, 2023)
17-41160580-G-A		not specified	Uncertain significance (Oct 06, 2021)
17-41160586-A-G		not specified	Uncertain significance (Sep 20, 2023)
17-41160618-T-C			Benign (Jul 13, 2018)
17-41160622-T-C		not specified	Uncertain significance (Jan 18, 2022)
17-41160630-C-G		not specified	Uncertain significance (May 05, 2023)
17-41160654-T-A		not specified	Uncertain significance (Jun 02, 2024)
17-41160667-C-T		not specified	Uncertain significance (Aug 08, 2023)
17-41160684-T-C		not specified	Likely benign (Nov 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTAP4-4	protein_coding	protein_coding	ENST00000390661	1	1074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.322	0.499	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.464	101	88.7	1.14	0.00000460	1085
Missense in Polyphen
Synonymous	-0.604	38	33.6	1.13	0.00000151	295
Loss of Function	0.571	0	0.380	0.00	1.56e-8	6

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: 0.646
• rvis_EVS: 1.79
• rvis_percentile_EVS: 96.89

Haploinsufficiency Scores

• pHI: 0.0470
• hipred: N
• hipred_score: 0.146

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	High
Cancer	Medium	Medium	Medium

Gene ontology

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