TUFT1

tuftelin 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:151540304-151583583

Links

ENSG00000143367 ∙ NCBI:7286 ∙ OMIM:600087 ∙ HGNC:12422 ∙ Uniprot:Q9NNX1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• woolly hair-skin fragility syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Woolly hair-skin fragility syndrome	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	36689522

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TUFT1 gene.

• Inborn genetic diseases (17 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUFT1 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	16	2	1

Variants in TUFT1

This is a list of pathogenic ClinVar variants found in the TUFT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151540427-G-A		Woolly hair-skin fragility syndrome	Pathogenic (Jun 13, 2023)
1-151561845-G-A			Benign (Dec 31, 2019)
1-151562109-A-G		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
1-151563908-A-G		Inborn genetic diseases	Uncertain significance (Nov 08, 2021)
1-151563986-A-C		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
1-151563987-G-C		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
1-151564549-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2022)
1-151564559-T-C		Inborn genetic diseases	Uncertain significance (Mar 29, 2022)
1-151564604-A-G		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
1-151566185-G-A		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
1-151566214-A-G		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
1-151566218-G-A		Inborn genetic diseases	Uncertain significance (Nov 14, 2023)
1-151569738-CG-C		Woolly hair-skin fragility syndrome	Pathogenic (Jun 13, 2023)
1-151569756-T-C		Inborn genetic diseases	Likely benign (Jan 08, 2024)
1-151574334-A-G		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
1-151574340-T-C		Inborn genetic diseases	Likely benign (Oct 18, 2021)
1-151574349-A-G		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
1-151574381-T-G		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
1-151574969-G-A		Inborn genetic diseases	Uncertain significance (Sep 20, 2023)
1-151578731-C-G		Inborn genetic diseases	Uncertain significance (May 27, 2022)
1-151578776-G-T			Uncertain significance (Nov 01, 2023)
1-151578801-G-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
1-151578810-G-A		Inborn genetic diseases	Uncertain significance (Nov 29, 2021)
1-151579685-G-A		Inborn genetic diseases	Likely benign (Jan 05, 2022)
1-151581018-G-A		Inborn genetic diseases	Uncertain significance (May 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUFT1	protein_coding	protein_coding	ENST00000368849	13	43279

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000106	0.998	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.897	186	224	0.831	0.0000122	2558
Missense in Polyphen		48	66.11	0.72606		857
Synonymous	1.04	69	80.9	0.853	0.00000421	696
Loss of Function	2.67	11	25.6	0.430	0.00000125	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the mineralization and structural organization of enamel. {ECO:0000250|UniProtKB:P27628}.

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.668
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.427
• hipred: N
• hipred_score: 0.328
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.621

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tuft1
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region 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); immune system phenotype; vision/eye phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: bone mineralization;intracellular signal transduction;odontogenesis
• Cellular component: extracellular region;cytoplasm
• Molecular function: protein binding;structural constituent of tooth enamel