KRTAP10-3

keratin associated protein 10-3, the group of Keratin associated proteins

Basic information

Region (hg38): 21:44557790-44558795

Previous symbols: [ "KRTAP18-3" ]

Links

ENSG00000212935 ∙ NCBI:386682 ∙ ∙ HGNC:22968 ∙ Uniprot:P60369 ∙ 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 KRTAP10-3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP10-3 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			33	5	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	6	1

Variants in KRTAP10-3

This is a list of pathogenic ClinVar variants found in the KRTAP10-3 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-44558091-C-A		not specified	Uncertain significance (Mar 05, 2024)
21-44558100-G-A		not specified	Uncertain significance (May 05, 2023)
21-44558102-C-T		not specified	Uncertain significance (Apr 24, 2024)
21-44558111-G-A		not specified	Uncertain significance (Jun 21, 2023)
21-44558117-C-T		not specified	Uncertain significance (Nov 16, 2022)
21-44558144-G-T		Autosomal recessive nonsyndromic hearing loss 98	Likely benign (Oct 05, 2020)
21-44558145-G-T		not specified	Uncertain significance (Dec 02, 2021)
21-44558147-C-T		not specified	Uncertain significance (Aug 04, 2023)
21-44558160-G-C		not specified	Uncertain significance (Jun 29, 2023)
21-44558169-T-A		not specified	Likely benign (Jun 01, 2023)
21-44558171-G-A		not specified	Uncertain significance (Sep 11, 2024)
21-44558175-C-T		not specified	Likely benign (Jun 01, 2023)
21-44558176-A-G			Likely benign (Sep 01, 2023)
21-44558190-A-G		not specified	Uncertain significance (Dec 04, 2024)
21-44558202-C-T		not specified	Uncertain significance (Jan 12, 2024)
21-44558211-T-C		not specified	Likely benign (Sep 20, 2024)
21-44558214-A-G		not specified	Likely benign (Aug 30, 2022)
21-44558223-C-G		not specified	Uncertain significance (Dec 26, 2023)
21-44558223-C-T		not specified	Uncertain significance (May 17, 2023)
21-44558228-C-T		not specified	Uncertain significance (Apr 25, 2023)
21-44558262-A-C		not specified	Uncertain significance (Sep 01, 2021)
21-44558276-C-T		not specified	Uncertain significance (Feb 10, 2022)
21-44558291-C-T		not specified	Uncertain significance (Feb 27, 2024)
21-44558297-G-C		not specified	Uncertain significance (Feb 10, 2022)
21-44558325-C-T		not specified	Uncertain significance (Jun 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTAP10-3	protein_coding	protein_coding	ENST00000391620	1	971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0235	0.785	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.68	187	133	1.41	0.00000825	1399
Missense in Polyphen		26	19.947	1.3034		204
Synonymous	-2.42	83	59.3	1.40	0.00000398	456
Loss of Function	0.957	3	5.40	0.556	2.39e-7	68

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: 0.551
• rvis_EVS: 2.13
• rvis_percentile_EVS: 97.94

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.112
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

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