KRT39

keratin 39, the group of Keratins, type I

Basic information

Region (hg38): 17:40958416-40966948

Links

ENSG00000196859 ∙ NCBI:390792 ∙ OMIM:616678 ∙ HGNC:32971 ∙ Uniprot:Q6A163 ∙ 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 KRT39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT39 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			28	3		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in KRT39

This is a list of pathogenic ClinVar variants found in the KRT39 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40958616-T-G			Uncertain significance (-)
17-40958635-T-A		not specified	Uncertain significance (Dec 06, 2022)
17-40958639-C-A		not specified	Uncertain significance (Dec 06, 2022)
17-40958663-T-C		not specified	Uncertain significance (Jul 14, 2021)
17-40958707-A-G		not specified	Uncertain significance (Feb 05, 2024)
17-40958728-G-T		not specified	Uncertain significance (Jun 10, 2024)
17-40958782-G-A		not specified	Uncertain significance (Jun 24, 2022)
17-40958830-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-40958834-T-C		not specified	Uncertain significance (Mar 31, 2024)
17-40958843-G-A		not specified	Likely benign (Nov 01, 2022)
17-40960297-C-G		not specified	Uncertain significance (Jan 17, 2024)
17-40960305-C-T		not specified	Uncertain significance (Mar 29, 2022)
17-40960335-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-40960345-C-T		not specified	Uncertain significance (Apr 08, 2024)
17-40960360-C-T		not specified	Uncertain significance (Jan 22, 2024)
17-40960371-T-C		not specified	Uncertain significance (Sep 17, 2021)
17-40960386-G-A		not specified	Uncertain significance (Apr 28, 2023)
17-40960462-G-A		not specified	Uncertain significance (Oct 12, 2022)
17-40962166-C-T		not specified	Uncertain significance (Jul 15, 2021)
17-40962208-C-A		not specified	Uncertain significance (Dec 20, 2021)
17-40962209-G-A		not specified	Uncertain significance (Mar 13, 2023)
17-40962220-A-G		not specified	Uncertain significance (Dec 14, 2023)
17-40962281-C-T		not specified	Uncertain significance (Feb 02, 2022)
17-40962406-G-A		not specified	Uncertain significance (Dec 03, 2021)
17-40962425-C-T		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT39	protein_coding	protein_coding	ENST00000355612	7	8476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.20e-13	0.115	125608	0	140	125748	0.000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.160	263	270	0.973	0.0000155	3208
Missense in Polyphen		83	86.277	0.96202		1128
Synonymous	0.429	100	106	0.947	0.00000580	958
Loss of Function	0.703	21	24.8	0.848	0.00000131	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000352	0.000352
Ashkenazi Jewish	0.00	0.00
East Asian	0.000489	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000630	0.000615
Middle Eastern	0.000489	0.000489
South Asian	0.00159	0.00154
Other	0.000490	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: 0.0820

Intolerance Scores

• loftool: 0.221
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.21

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.213

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krt39

Gene ontology

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