KRTAP9-3

keratin associated protein 9-3, the group of Keratin associated proteins

Basic information

Region (hg38): 17:41232449-41233454

Links

ENSG00000204873 ∙ NCBI:83900 ∙ ∙ HGNC:16927 ∙ Uniprot:Q9BYQ3 ∙ 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 KRTAP9-3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP9-3 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						0
missense			18	4		22
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	4	0

Variants in KRTAP9-3

This is a list of pathogenic ClinVar variants found in the KRTAP9-3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-41232558-G-C		not specified	Likely benign (Jan 06, 2023)
17-41232566-C-G		not specified	Uncertain significance (Oct 07, 2024)
17-41232574-A-T		not specified	Uncertain significance (Sep 30, 2024)
17-41232575-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-41232580-T-C		not specified	Uncertain significance (May 06, 2024)
17-41232581-G-A		not specified	Uncertain significance (Jan 30, 2024)
17-41232592-C-T		not specified	Uncertain significance (May 11, 2022)
17-41232640-T-C		not specified	Uncertain significance (Mar 22, 2023)
17-41232644-A-G		not specified	Likely benign (Feb 27, 2024)
17-41232650-C-T		not specified	Uncertain significance (Oct 30, 2023)
17-41232665-C-A		not specified	Uncertain significance (Oct 13, 2023)
17-41232680-C-A		not specified	Uncertain significance (Jul 13, 2021)
17-41232698-G-A		not specified	Uncertain significance (Dec 02, 2021)
17-41232713-G-A		not specified	Uncertain significance (Aug 28, 2023)
17-41232736-C-T		not specified	Uncertain significance (Nov 13, 2024)
17-41232737-C-G		not specified	Uncertain significance (Apr 18, 2023)
17-41232754-T-C		not specified	Uncertain significance (Sep 15, 2021)
17-41232766-A-C		not specified	Uncertain significance (Nov 08, 2024)
17-41232775-C-G		not specified	Uncertain significance (Jul 14, 2023)
17-41232779-G-A		not specified	Uncertain significance (Feb 02, 2024)
17-41232785-C-T		not specified	Uncertain significance (Dec 26, 2023)
17-41232789-T-G		not specified	Uncertain significance (Dec 26, 2023)
17-41232809-G-A		not specified	Uncertain significance (Feb 01, 2023)
17-41232814-T-C		not specified	Uncertain significance (May 14, 2024)
17-41232830-G-C		not specified	Likely benign (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTAP9-3	protein_coding	protein_coding	ENST00000411528	1	991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.54	122	82.6	1.48	0.00000386	1050
Missense in Polyphen		27	23.451	1.1514		311
Synonymous	-2.87	50	30.0	1.67	0.00000135	290
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

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.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.187
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.0747
• hipred: N
• hipred_score: 0.146
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.560

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