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
wooly hair, autosomal recessive 3 (Moderate), mode of inheritance: AR

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.

not_specified (68 variants)
not_provided (31 variants)
Wooly_hair,_autosomal_recessive_3 (3 variants)
KRT25-related_disorder (3 variants)
Hypotrichosis_8 (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. These statistics are base on transcript: NM_000181534.4. 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				8 clinvar	4 clinvar	12
missense	2 clinvar		67 clinvar	8 clinvar	3 clinvar	80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	2	0	67	16	7

Highest pathogenic variant AF is 0.0000210649

Loading clinvar variants...

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
ghis

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