KRT12

keratin 12, the group of Keratins, type I

Basic information

Region (hg38): 17:40861303-40867223

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.

Inborn_genetic_diseases (43 variants)
not_provided (41 variants)
Corneal_dystrophy,_Meesmann,_1 (13 variants)
KRT12-related_disorder (6 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. These statistics are base on transcript: NM_000000223.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	3 clinvar	6
missense	8 clinvar	3 clinvar	53 clinvar	6 clinvar	4 clinvar	74
nonsense			3 clinvar			3
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	8	3	58	9	7

Highest pathogenic variant AF is 0.000026643898

Loading clinvar variants...

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
ghis

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