KRT40

keratin 40, the group of Keratins, type I

Basic information

Region (hg38): 17:40977715-40987135

Links

ENSG00000204889 ∙ NCBI:125115 ∙ OMIM:616679 ∙ HGNC:26707 ∙ Uniprot:Q6A162 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT40 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						0
missense			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in KRT40

This is a list of pathogenic ClinVar variants found in the KRT40 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40978217-C-T		not specified	Uncertain significance (Dec 21, 2023)
17-40978241-A-G		not specified	Uncertain significance (Dec 13, 2022)
17-40978856-G-T		not specified	Uncertain significance (Apr 24, 2024)
17-40978900-C-T		not specified	Uncertain significance (Oct 25, 2023)
17-40978904-C-G		not specified	Uncertain significance (Jan 20, 2023)
17-40978915-C-T		not specified	Uncertain significance (Oct 20, 2021)
17-40978924-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-40978947-G-C		not specified	Uncertain significance (Dec 03, 2021)
17-40980805-G-A		not specified	Uncertain significance (Jan 10, 2023)
17-40980816-A-G		not specified	Uncertain significance (Mar 29, 2023)
17-40980826-C-G		not specified	Uncertain significance (Apr 08, 2024)
17-40980826-C-T		not specified	Uncertain significance (Oct 12, 2022)
17-40980877-C-T		not specified	Uncertain significance (Jul 21, 2021)
17-40981010-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-40981039-G-A		not specified	Uncertain significance (Oct 25, 2022)
17-40981055-G-A		not specified	Uncertain significance (Nov 13, 2023)
17-40981073-T-C		not specified	Uncertain significance (Nov 17, 2023)
17-40981111-C-T		not specified	Uncertain significance (Mar 18, 2024)
17-40982314-T-C		not specified	Uncertain significance (Aug 15, 2023)
17-40982366-C-T		not specified	Uncertain significance (May 04, 2022)
17-40982404-C-G		not specified	Uncertain significance (Feb 02, 2022)
17-40982436-C-A		not specified	Uncertain significance (May 23, 2023)
17-40983073-T-C		not specified	Uncertain significance (Mar 15, 2024)
17-40983867-T-C		not specified	Uncertain significance (Oct 12, 2021)
17-40983883-T-C		not specified	Uncertain significance (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT40	protein_coding	protein_coding	ENST00000377755	7	9420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.10e-10	0.256	125655	0	45	125700	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.436	254	235	1.08	0.0000134	2796
Missense in Polyphen		96	79.986	1.2002		1015
Synonymous	-0.306	106	102	1.04	0.00000629	825
Loss of Function	0.719	16	19.4	0.824	0.00000100	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000752	0.000729
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000167	0.000163
South Asian	0.000332	0.000327
Other	0.000502	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in late hair differentiation.
• Pathway: Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology (Consensus)

Recessive Scores

• pRec: 0.0872

Intolerance Scores

• loftool: 0.176
• rvis_EVS: 3.2
• rvis_percentile_EVS: 99.35

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0352

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krt40

Gene ontology

• Biological process: keratinization;cornification
• Cellular component: cytosol;intermediate filament
• Molecular function: structural molecule activity;protein binding