KRTAP6-3

keratin associated protein 6-3, the group of Keratin associated proteins

Basic information

Region (hg38): 21:30592439-30593075

Links

ENSG00000212938 ∙ NCBI:337968 ∙ ∙ HGNC:18933 ∙ Uniprot:Q3LI67 ∙ 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 KRTAP6-3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTAP6-3 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			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in KRTAP6-3

This is a list of pathogenic ClinVar variants found in the KRTAP6-3 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-30592469-G-A		not specified	Uncertain significance (Oct 25, 2023)
21-30592469-G-T		not specified	Uncertain significance (Oct 05, 2022)
21-30592555-G-A		not specified	Uncertain significance (Jun 10, 2024)
21-30592570-G-T		not specified	Uncertain significance (May 22, 2023)
21-30592582-G-A		not specified	Uncertain significance (Sep 22, 2023)
21-30592588-G-T			Benign (Jul 06, 2018)
21-30592596-T-G		not specified	Uncertain significance (Aug 02, 2021)
21-30592710-C-T		not specified	Uncertain significance (Sep 22, 2023)
21-30592726-G-A		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTAP6-3	protein_coding	protein_coding	ENST00000391624	1	636

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.512	0.426	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.153	50	53.1	0.941	0.00000245	625
Missense in Polyphen
Synonymous	-0.247	28	26.4	1.06	0.00000151	210
Loss of Function	1.32	0	2.04	0.00	8.47e-8	31

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.

Haploinsufficiency Scores

• pHI: 0.381
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000104

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;intermediate filament