KRT20

keratin 20, the group of Keratins, type I

Basic information

Region (hg38): 17:40875889-40885242

Links

ENSG00000171431 ∙ NCBI:54474 ∙ OMIM:608218 ∙ HGNC:20412 ∙ Uniprot:P35900 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT20 gene.

• not_specified (62 variants)
• not_provided (7 variants)
• KRT20-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT20 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000019010.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	2	4
missense			62	3	1	66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	5	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT20	protein_coding	protein_coding	ENST00000167588	8	9287

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.08e-11	0.154	125645	1	102	125748	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.369	227	243	0.933	0.0000143	2774
Missense in Polyphen		72	76.911	0.93615		924
Synonymous	-0.560	104	97.0	1.07	0.00000574	821
Loss of Function	0.559	17	19.7	0.864	9.85e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000830	0.000824
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000335	0.000334
Middle Eastern	0.000217	0.000217
South Asian	0.00117	0.00105
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine (By similarity). {ECO:0000250, ECO:0000269|PubMed:12857878, ECO:0000269|PubMed:16608857}.
• Pathway: Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology (Consensus)

Recessive Scores

• pRec: 0.255

Intolerance Scores

• loftool: 0.210
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.336
• hipred: N
• hipred_score: 0.169

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krt20

Gene ontology

• Biological process: apoptotic process;cellular response to starvation;keratinization;intermediate filament organization;regulation of protein secretion;cornification
• Cellular component: cytoplasm;cytosol;intermediate filament
• Molecular function: structural constituent of cytoskeleton;protein binding