KRT6B

keratin 6B, the group of Keratins, type II

Basic information

Region (hg38): 12:52446651-52452146

Previous symbols: [ "KRTL1" ]

Links

ENSG00000185479 ∙ NCBI:3854 ∙ OMIM:148042 ∙ HGNC:6444 ∙ Uniprot:P04259 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pachyonychia congenita 4 (Strong), mode of inheritance: AD
• pachyonychia congenita 4 (Moderate), mode of inheritance: AD
• pachyonychia congenita 4 (Strong), mode of inheritance: AD
• pachyonychia congenita (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pachyonychia congenita 4	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dental; Dermatologic	9618173; 11886499; 20301457

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT6B gene.

• not provided (2 variants)
• Pachyonychia congenita 4 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT6B 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				19	14	33
missense	1	2	62	9	13	87
nonsense						0
start loss						0
frameshift						0
inframe indel	1					1
splice donor/acceptor (+/-2bp)						0
splice region			1	3	3	7
non coding				6	6	12
Total	2	2	62	34	33

Variants in KRT6B

This is a list of pathogenic ClinVar variants found in the KRT6B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-52447220-G-A			Benign (Nov 02, 2023)
12-52447224-G-A			Uncertain significance (Jun 28, 2022)
12-52447226-G-A			Likely benign (Apr 15, 2023)
12-52447245-G-C		Inborn genetic diseases	Uncertain significance (Apr 18, 2023)
12-52447252-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 13, 2023)
12-52447260-A-G			Benign (Jan 16, 2024)
12-52447265-G-C			Uncertain significance (Jan 02, 2020)
12-52447276-C-T			Uncertain significance (Jun 01, 2019)
12-52447281-G-A		Inborn genetic diseases	Likely benign (Aug 22, 2023)
12-52447292-G-T			Benign (Jun 22, 2022)
12-52447336-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 11, 2024)
12-52447337-G-A			Benign (Dec 11, 2023)
12-52447362-C-T		Inborn genetic diseases	Uncertain significance (Nov 15, 2021)
12-52447375-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 07, 2024)
12-52447390-C-T		Pachyonychia congenita 4	Benign (Jan 29, 2024)
12-52447391-G-A			Benign/Likely benign (Jun 01, 2024)
12-52447395-T-C		KRT6B-related disorder	Benign (Jan 22, 2024)
12-52447401-C-T			Likely benign (May 05, 2022)
12-52447409-G-A			Benign (Sep 20, 2022)
12-52447419-A-G		Inborn genetic diseases	Uncertain significance (Aug 21, 2023)
12-52447439-G-C			Likely benign (Oct 26, 2022)
12-52447525-A-G			Benign (Jan 16, 2023)
12-52447557-C-T			Likely benign (Oct 11, 2023)
12-52447579-G-A			Likely benign (Nov 17, 2022)
12-52447765-G-A			Benign (Mar 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT6B	protein_coding	protein_coding	ENST00000252252	9	5476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.52e-10	0.224	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.23	423	312	1.36	0.0000198	3631
Missense in Polyphen		129	101.24	1.2741		1393
Synonymous	-1.70	155	130	1.19	0.00000843	1138
Loss of Function	0.657	16	19.1	0.838	8.51e-7	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000569	0.000568
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000217	0.000217
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Keratinization;Developmental Biology (Consensus)

Intolerance Scores

• loftool: 0.110
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.25

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.318
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.458

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krt6b
• Phenotype: digestive/alimentary phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: cytoskeleton organization;ectoderm development;keratinization;cornification
• Cellular component: cytosol;keratin filament;extracellular exosome
• Molecular function: structural constituent of cytoskeleton;protein binding