KRT25

keratin 25, the group of Keratins, type I

Basic information

Region (hg38): 17:40748021-40755331

Previous symbols: [ "KRT25A" ]

Links

ENSG00000204897 ∙ NCBI:147183 ∙ OMIM:616646 ∙ HGNC:30839 ∙ Uniprot:Q7Z3Z0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• wooly hair, autosomal recessive 3 (Strong), mode of inheritance: AR
• isolated familial wooly hair disorder (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Woolly hair, autosomal recessive 3	AR	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	Dermatologic	26160856

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT25 gene.

• Wooly hair, autosomal recessive 3 (1 variants)
• Autosomal Recessive Hypotrichosis with Woolly Hair (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT25 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				9	3	12
missense	1		32	4	5	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	6	9
Total	1	0	32	16	14

Variants in KRT25

This is a list of pathogenic ClinVar variants found in the KRT25 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40748313-C-G			Uncertain significance (Sep 15, 2022)
17-40748384-G-C		not specified	Uncertain significance (May 27, 2022)
17-40749225-T-G			Benign (Nov 12, 2018)
17-40749270-T-C		not specified	Uncertain significance (Jan 04, 2024)
17-40749315-A-C		not specified	Uncertain significance (Apr 01, 2024)
17-40749339-G-A			Likely benign (Mar 08, 2023)
17-40750466-C-T			Benign (Dec 21, 2023)
17-40750519-C-T		not specified	Uncertain significance (Jun 21, 2023)
17-40750538-C-T			Likely benign (Nov 18, 2023)
17-40750548-G-C			Benign (Nov 24, 2023)
17-40750551-C-A		not specified	Uncertain significance (Dec 19, 2022)
17-40750561-T-C		not specified	Likely benign (Jun 02, 2024)
17-40750565-G-A			Likely benign (Sep 27, 2022)
17-40750593-T-G		not specified	Uncertain significance (Dec 28, 2022)
17-40750961-A-G		Hypotrichosis 8 • Wooly hair, autosomal recessive 3	Pathogenic (Oct 01, 2015)
17-40750979-A-G		not specified	Uncertain significance (Jul 21, 2021)
17-40751020-A-C		not specified	Conflicting classifications of pathogenicity (Jul 05, 2023)
17-40751090-A-G			Likely benign (Jun 08, 2022)
17-40751168-C-G		not specified	Uncertain significance (Apr 22, 2024)
17-40751196-C-T			Benign (Jan 08, 2024)
17-40751197-G-A			Uncertain significance (Oct 17, 2022)
17-40751260-C-T		not specified	Uncertain significance (Oct 22, 2021)
17-40751265-G-A		not specified	Uncertain significance (Jun 24, 2022)
17-40751280-T-G			Benign (Jan 18, 2024)
17-40751284-C-A		Autosomal Recessive Hypotrichosis with Woolly Hair • Wooly hair, autosomal recessive 3	Pathogenic (Feb 20, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT25	protein_coding	protein_coding	ENST00000312150	8	7312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.65e-9	0.600	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.166	248	255	0.971	0.0000142	2928
Missense in Polyphen		91	98.38	0.92499		1183
Synonymous	0.143	101	103	0.982	0.00000618	903
Loss of Function	1.21	16	22.2	0.722	0.00000119	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000843	0.000839
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000239	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.000372	0.000359
Other	0.000843	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for the proper assembly of type I and type II keratin protein complexes and formation of keratin intermediate filaments in the inner root sheath (irs) (By similarity). Plays a role in the cytoskeleton organization (PubMed:26902920). {ECO:0000250|UniProtKB:Q8VCW2, ECO:0000269|PubMed:26902920}.
• Pathway: Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.267
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.194
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0616

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krt25
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: cytoskeleton organization;aging;hair follicle morphogenesis;keratinization;hair cycle;intermediate filament organization;cornification
• Cellular component: cytosol;intermediate filament;extracellular exosome
• Molecular function: molecular_function;structural molecule activity;protein heterodimerization activity