KRT3

keratin 3, the group of Keratins, type II

Basic information

Region (hg38): 12:52789685-52796117

Links

ENSG00000186442 ∙ NCBI:3850 ∙ OMIM:148043 ∙ HGNC:6440 ∙ Uniprot:P12035 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Meesmann corneal dystrophy (Supportive), mode of inheritance: AD
• corneal dystrophy, Meesmann, 1 (Strong), mode of inheritance: AD
• corneal dystrophy, Meesmann, 1 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Corneal dystrophy, Meesmann, 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	Ophthalmologic	9171831

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT3 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				11	6	17
missense		2	37	5	8	52
nonsense						0
start loss						0
frameshift						0
inframe indel					2	2
splice donor/acceptor (+/-2bp)					1	1
splice region				1	2	3
non coding					1	1
Total	0	2	37	16	18

Variants in KRT3

This is a list of pathogenic ClinVar variants found in the KRT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-52790076-T-A		not specified	Uncertain significance (Dec 30, 2023)
12-52790088-A-T		not specified	Uncertain significance (Aug 12, 2024)
12-52790098-C-T			Benign (Nov 10, 2023)
12-52790102-G-A			Likely benign (Nov 15, 2023)
12-52790111-C-T			Benign (Jan 14, 2023)
12-52790127-C-T		KRT3-related disorder	Likely benign (Sep 19, 2023)
12-52790167-C-CGCTGCCACCGCTGAAACCGCT			Benign (Jan 29, 2024)
12-52790176-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-52790205-C-T		not specified	Uncertain significance (Nov 27, 2024)
12-52790219-A-G			Likely benign (Jun 08, 2018)
12-52790221-C-T		not specified	Likely benign (Aug 19, 2023)
12-52790232-C-G		not specified	Uncertain significance (Mar 20, 2024)
12-52790259-C-T		not specified	Uncertain significance (Jan 19, 2022)
12-52790265-C-A		not specified	Uncertain significance (Dec 13, 2022)
12-52790268-A-C		not specified	Uncertain significance (Aug 11, 2022)
12-52790272-C-T		not specified	Uncertain significance (Dec 19, 2022)
12-52790276-T-C			Benign (Mar 21, 2023)
12-52790289-C-T		not specified	Uncertain significance (Jul 14, 2021)
12-52790292-A-G		not specified	Uncertain significance (Apr 07, 2023)
12-52790302-C-G		not specified	Uncertain significance (May 01, 2024)
12-52790355-A-G		not specified	Uncertain significance (Oct 25, 2023)
12-52790363-G-C		KRT3-related disorder	Benign (Jun 07, 2019)
12-52790835-T-TA			Benign (Jan 29, 2024)
12-52791200-G-A			Benign (Nov 15, 2018)
12-52791214-C-A		Corneal dystrophy, Meesmann, 2	Likely pathogenic (Jan 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT3	protein_coding	protein_coding	ENST00000417996	9	6433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.00e-10	0.289	125674	1	73	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0680	369	373	0.990	0.0000226	4073
Missense in Polyphen		100	109.08	0.91673		1513
Synonymous	-1.54	179	155	1.16	0.0000101	1298
Loss of Function	0.778	16	19.7	0.811	8.44e-7	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000890	0.000882
Ashkenazi Jewish	0.00	0.00
East Asian	0.00104	0.00103
Finnish	0.00	0.00
European (Non-Finnish)	0.000189	0.000185
Middle Eastern	0.00104	0.00103
South Asian	0.000393	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Keratinization;Developmental Biology (Consensus)

Intolerance Scores

• loftool: 0.164
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.65

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.112
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.180

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: epithelial cell differentiation;keratinization;intermediate filament cytoskeleton organization;cornification
• Cellular component: cytosol;intermediate filament;keratin filament;extracellular exosome
• Molecular function: structural molecule activity