KRT15

keratin 15, the group of Keratins, type I|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:41513744-41522529

Links

ENSG00000171346 ∙ NCBI:3866 ∙ OMIM:148030 ∙ HGNC:6421 ∙ Uniprot:P19012 ∙ 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 KRT15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT15 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			24	1	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	25	2	1

Variants in KRT15

This is a list of pathogenic ClinVar variants found in the KRT15 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-41514055-G-T		not specified	Likely benign (Mar 03, 2022)
17-41515499-C-T		not specified	Uncertain significance (Sep 29, 2022)
17-41515509-C-T		not specified	Uncertain significance (Oct 26, 2022)
17-41515514-T-C		not specified	Uncertain significance (Dec 05, 2022)
17-41515526-C-T		not specified	Uncertain significance (Feb 08, 2023)
17-41515589-T-C		not specified	Uncertain significance (Oct 03, 2022)
17-41515636-C-T			Likely benign (Mar 28, 2018)
17-41515675-G-C		not specified	Uncertain significance (Jan 16, 2024)
17-41515888-G-C		not specified	Uncertain significance (May 31, 2023)
17-41516124-C-T		not specified	Uncertain significance (Feb 01, 2023)
17-41516161-C-G		not specified	Uncertain significance (Dec 17, 2023)
17-41516253-A-G		not specified	Uncertain significance (Apr 18, 2023)
17-41516818-T-C		not specified	Uncertain significance (Oct 06, 2023)
17-41516879-T-C		not specified	Uncertain significance (Feb 23, 2023)
17-41516882-C-A		not specified	Uncertain significance (Dec 02, 2021)
17-41516948-C-T		not specified	Uncertain significance (Apr 25, 2023)
17-41517116-T-C		not specified	Uncertain significance (Apr 22, 2022)
17-41518338-G-A		not specified	Uncertain significance (Jan 26, 2022)
17-41518355-T-C		not specified	Uncertain significance (Dec 13, 2021)
17-41518374-C-T		not specified	Uncertain significance (Aug 22, 2023)
17-41518577-C-T		not specified	Uncertain significance (May 20, 2024)
17-41518653-C-T		not specified	Uncertain significance (Dec 11, 2023)
17-41518703-C-T			Uncertain significance (Jan 01, 2023)
17-41518706-C-T		not specified	Uncertain significance (Dec 14, 2022)
17-41518733-C-T			Benign (Apr 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT15	protein_coding	protein_coding	ENST00000254043	8	8787

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.39e-16	0.00435	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.000895	268	268	1.00	0.0000165	2962
Missense in Polyphen		105	103.02	1.0192		1238
Synonymous	-0.768	121	111	1.09	0.00000714	934
Loss of Function	-0.335	23	21.3	1.08	0.00000128	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000661	0.000651
Ashkenazi Jewish	0.00	0.00
East Asian	0.00152	0.00152
Finnish	0.00	0.00
European (Non-Finnish)	0.000273	0.000273
Middle Eastern	0.00152	0.00152
South Asian	0.000650	0.000621
Other	0.000860	0.000815

dbNSFP

Source: dbNSFP

• Pathway: Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology (Consensus)

Recessive Scores

• pRec: 0.213

Intolerance Scores

• loftool: 0.181
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.66

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.172
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.572

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Krt15
• Phenotype: homeostasis/metabolism phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: cytoskeleton organization;epidermis development;keratinization;cornification
• Cellular component: nucleus;cytosol;intermediate filament;extracellular exosome
• Molecular function: structural constituent of cytoskeleton;protein binding;scaffold protein binding