KRT13

keratin 13, the group of Keratins, type I

Basic information

Region (hg38): 17:41500980-41505705

Links

ENSG00000171401 ∙ NCBI:3860 ∙ OMIM:148065 ∙ HGNC:6415 ∙ Uniprot:P13646 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary mucosal leukokeratosis (Supportive), mode of inheritance: AD
• white sponge nevus 2 (Moderate), mode of inheritance: AD
• white sponge nevus 2 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
White sponge nevus 2	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	Dermatologic	7493031

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT13 gene.

• White sponge nevus 2 (57 variants)
• not provided (27 variants)
• Inborn genetic diseases (25 variants)
• White sponge nevus 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT13 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			3	3	7	13
missense			29	2	19	50
nonsense				1		1
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					4	4
non coding			7	1	11	19
Total	0	0	39	7	38

Variants in KRT13

This is a list of pathogenic ClinVar variants found in the KRT13 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-41500982-A-G		White sponge nevus 2	Benign (Jan 13, 2018)
17-41500988-G-A		White sponge nevus 2	Benign (Jan 13, 2018)
17-41501028-G-C		White sponge nevus 2	Uncertain significance (Jan 13, 2018)
17-41501081-C-T		White sponge nevus 2	Uncertain significance (Jan 12, 2018)
17-41501085-C-A		White sponge nevus 2	Benign (May 12, 2021)
17-41501086-G-A		White sponge nevus 2	Benign (May 12, 2021)
17-41501094-A-G		White sponge nevus 2	Uncertain significance (Jan 13, 2018)
17-41501171-G-A		White sponge nevus 2	Uncertain significance (Jan 12, 2018)
17-41501182-T-G		White sponge nevus 2	Uncertain significance (Jan 13, 2018)
17-41501237-G-A		White sponge nevus 2	Uncertain significance (Jan 13, 2018)
17-41501267-G-A		White sponge nevus 2	Benign (Jan 13, 2018)
17-41501277-A-C		KRT13-related disorder	Likely benign (Apr 10, 2019)
17-41501281-C-T		White sponge nevus 2	Benign (Jan 13, 2018)
17-41501283-G-A		White sponge nevus 2	Uncertain significance (Jan 13, 2018)
17-41501338-G-C		White sponge nevus 2	Uncertain significance (Jan 12, 2018)
17-41501347-C-T		White sponge nevus 2	Benign (Dec 01, 2023)
17-41501357-C-T		White sponge nevus 2 • KRT13-related disorder	Benign/Likely benign (Jan 03, 2020)
17-41501358-G-A		Inborn genetic diseases	Uncertain significance (Jul 15, 2021)
17-41501359-C-CT			Benign (Dec 05, 2018)
17-41501711-T-C		KRT13-related disorder	Benign (May 08, 2019)
17-41502347-C-T			Benign (May 24, 2021)
17-41502378-C-T		Inborn genetic diseases	Uncertain significance (Jan 26, 2023)
17-41502380-T-A		White sponge nevus 2	Likely benign (Jan 13, 2018)
17-41502391-G-A		White sponge nevus 2	Benign (Jan 13, 2018)
17-41502398-C-T		White sponge nevus 2 • Inborn genetic diseases	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT13	protein_coding	protein_coding	ENST00000246635	8	4725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000641	0.980	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.516	303	279	1.09	0.0000190	2962
Missense in Polyphen		129	116.23	1.1098		1367
Synonymous	-0.938	124	111	1.11	0.00000755	945
Loss of Function	2.06	8	17.2	0.465	7.55e-7	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000264
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000233	0.000231
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: White sponge nevus 2 (WSN2) [MIM:615785]: A rare disorder characterized by the presence of soft, white, and spongy plaques in the oral mucosa. The characteristic histopathologic features are epithelial thickening, parakeratosis, and vacuolization of the suprabasal layer of oral epithelial keratinocytes. Less frequently the mucous membranes of the nose, esophagus, genitalia and rectum are involved. {ECO:0000269|PubMed:10561721, ECO:0000269|PubMed:11379896, ECO:0000269|PubMed:14600690, ECO:0000269|PubMed:7493031}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Estrogen signaling pathway - Homo sapiens (human);Vitamin D Receptor Pathway;Keratinization;Developmental Biology (Consensus)

Intolerance Scores

• loftool: 0.0615
• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.1

Haploinsufficiency Scores

• pHI: 0.0953
• hipred: N
• hipred_score: 0.131
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krt13

Gene ontology

• Biological process: cytoskeleton organization;keratinization;cornification
• Cellular component: nucleus;cytosol;keratin filament;intermediate filament cytoskeleton;extracellular exosome
• Molecular function: structural molecule activity;protein binding