KRT12

keratin 12, the group of Keratins, type I

Basic information

Region (hg38): 17:40861302-40867223

Links

ENSG00000187242 ∙ NCBI:3859 ∙ OMIM:601687 ∙ HGNC:6414 ∙ Uniprot:Q99456 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Meesmann corneal dystrophy (Supportive), mode of inheritance: AD
• corneal dystrophy, Meesmann, 1 (Definitive), 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
Meesmann corneal dystrophy 1	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; 18661274; 20577595

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT12 gene.

• not provided (32 variants)
• Inborn genetic diseases (10 variants)
• Corneal dystrophy, Meesmann, 1 (7 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT12 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	6
missense	1	2	11	3	6	23
nonsense			2			2
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	2	16	6	9

Highest pathogenic variant AF is 0.0000328

Variants in KRT12

This is a list of pathogenic ClinVar variants found in the KRT12 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40861690-G-C			Uncertain significance (Nov 07, 2022)
17-40861710-T-C		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
17-40861722-T-C		KRT12-related disorder	Likely benign (Nov 02, 2023)
17-40862557-C-G		KRT12-related disorder	Likely benign (Jun 05, 2020)
17-40863123-C-T			Uncertain significance (Aug 24, 2022)
17-40863130-C-T		Inborn genetic diseases	Uncertain significance (Jul 13, 2021)
17-40863141-A-C			not provided (-)
17-40863150-C-G			not provided (-)
17-40863153-T-C			not provided (-)
17-40863154-A-C		Corneal dystrophy, Meesmann, 1	Pathogenic (Dec 01, 1997)
17-40863162-A-C			not provided (-)
17-40863163-T-C			not provided (-)
17-40863210-A-C			Benign (Dec 28, 2023)
17-40863258-A-G		Corneal dystrophy, Meesmann, 1	Likely pathogenic (Jan 01, 2022)
17-40863279-ACCTGGGACAGCT-A		Corneal dystrophy, Meesmann, 1	Uncertain significance (Sep 24, 2021)
17-40863288-A-G		Corneal dystrophy, Meesmann, 1	Uncertain significance (Feb 11, 2021)
17-40863336-G-A		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
17-40863564-T-A		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
17-40863585-C-CTA		not specified	Uncertain significance (May 04, 2022)
17-40863592-C-A		Corneal dystrophy, Meesmann, 1	Uncertain significance (Dec 31, 2021)
17-40863707-T-C		Inborn genetic diseases	Uncertain significance (Sep 20, 2023)
17-40863756-C-T		Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
17-40863770-A-G		KRT12-related disorder	Likely benign (Feb 01, 2023)
17-40863800-C-A		Inborn genetic diseases	Uncertain significance (May 25, 2022)
17-40864846-A-G		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT12	protein_coding	protein_coding	ENST00000251643	8	5908

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.53e-14	0.0348	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.570	266	293	0.906	0.0000182	3187
Missense in Polyphen		92	108.08	0.85124		1282
Synonymous	1.36	108	127	0.847	0.00000861	1034
Loss of Function	0.346	22	23.8	0.923	0.00000136	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000720	0.000718
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000300	0.000290
Middle Eastern	0.000272	0.000272
South Asian	0.000196	0.000196
Other	0.000503	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a unique role in maintaining the normal corneal epithelial function. Together with KRT3, essential for the maintenance of corneal epithelium integrity (By similarity). {ECO:0000250}.
• Pathway: Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology (Consensus)

Recessive Scores

• pRec: 0.215

Intolerance Scores

• loftool: 0.199
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.2

Haploinsufficiency Scores

• pHI: 0.219
• hipred: N
• hipred_score: 0.367

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krt12
• Phenotype: normal phenotype; vision/eye phenotype

Gene ontology

• Biological process: visual perception;keratinization;cornification
• Cellular component: cytosol;intermediate filament;extracellular exosome
• Molecular function: structural molecule activity