KRTAP5-3

keratin associated protein 5-3, the group of Keratin associated proteins

Basic information

Region (hg38): 11:1607565-1608463

Links

ENSG00000196224 ∙ NCBI:387266 ∙ ∙ HGNC:23598 ∙ Uniprot:Q6L8H2 ∙ 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 KRTAP5-3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP5-3 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in KRTAP5-3

This is a list of pathogenic ClinVar variants found in the KRTAP5-3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-1607721-C-T		not specified	Uncertain significance (Jan 16, 2024)
11-1607794-T-G		not specified	Uncertain significance (Aug 21, 2024)
11-1607813-T-C			Likely benign (Mar 01, 2023)
11-1607847-C-T		not specified	Uncertain significance (Oct 25, 2022)
11-1607869-G-A		not specified	Uncertain significance (Apr 24, 2023)
11-1607940-C-G		not specified	Uncertain significance (Apr 22, 2022)
11-1607946-T-G		not specified	Uncertain significance (Oct 25, 2024)
11-1608022-C-T		not specified	Uncertain significance (Mar 27, 2023)
11-1608030-C-G		not specified	Uncertain significance (Mar 27, 2023)
11-1608076-A-T		not specified	Uncertain significance (Apr 07, 2023)
11-1608103-C-T		not specified	Uncertain significance (Aug 05, 2024)
11-1608124-C-G		not specified	Uncertain significance (Feb 13, 2024)
11-1608130-C-G		not specified	Uncertain significance (Oct 07, 2024)
11-1608160-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-1608248-G-C		not specified	Uncertain significance (Jul 06, 2021)
11-1608253-C-A		not specified	Uncertain significance (Nov 10, 2022)
11-1608253-C-T		not specified	Uncertain significance (Aug 02, 2022)
11-1608276-A-C		not specified	Uncertain significance (Nov 09, 2021)
11-1608351-G-T		not specified	Uncertain significance (Nov 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTAP5-3	protein_coding	protein_coding	ENST00000399685	1	899

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.164	0.653	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.108	124	121	1.03	0.00000609	1524
Missense in Polyphen
Synonymous	-0.878	59	51.0	1.16	0.00000264	463
Loss of Function	0.782	1	2.27	0.440	1.00e-7	51

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 protein (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: 0.755
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0790

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