TTC1

tetratricopeptide repeat domain 1, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 5:160009112-160065543

Links

ENSG00000113312 ∙ NCBI:7265 ∙ OMIM:601963 ∙ HGNC:12391 ∙ Uniprot:Q99614 ∙ 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 TTC1 gene.

• Inborn genetic diseases (10 variants)
• Abnormal brain morphology (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC1 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		1	10			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	1	10	0	0

Variants in TTC1

This is a list of pathogenic ClinVar variants found in the TTC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-160010656-G-A		not specified	Uncertain significance (Mar 04, 2024)
5-160010670-G-A		not specified	Uncertain significance (Aug 05, 2023)
5-160010698-A-G		not specified	Uncertain significance (Mar 17, 2023)
5-160010711-G-T		not specified	Uncertain significance (Dec 28, 2022)
5-160010736-T-A		not specified	Uncertain significance (Dec 17, 2023)
5-160010752-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-160010815-A-G		not specified	Uncertain significance (Apr 20, 2023)
5-160036729-G-A		not specified	Uncertain significance (Apr 20, 2023)
5-160036781-G-C		not specified	Uncertain significance (Dec 27, 2022)
5-160043127-T-C			Benign (Jun 28, 2018)
5-160043151-A-G		not specified	Uncertain significance (Feb 05, 2024)
5-160049577-C-T		not specified	Uncertain significance (Mar 01, 2023)
5-160049615-A-G		not specified	Uncertain significance (Sep 12, 2023)
5-160049649-G-A		not specified	Uncertain significance (Dec 19, 2023)
5-160051178-T-C		not specified	Uncertain significance (Feb 22, 2023)
5-160064958-G-A		not specified	Uncertain significance (May 11, 2022)
5-160064970-T-G		Abnormal brain morphology	Likely pathogenic (-)
5-160064999-C-G		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC1	protein_coding	protein_coding	ENST00000231238	7	56431

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000255	0.757	125692	0	55	125747	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.659	125	148	0.847	0.00000719	1940
Missense in Polyphen		19	33.847	0.56135		426
Synonymous	0.437	54	58.2	0.927	0.00000334	495
Loss of Function	1.23	11	16.4	0.672	8.39e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000873	0.0000873
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00164	0.00163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000997	0.0000967
Middle Eastern	0.00164	0.00163
South Asian	0.000199	0.000196
Other	0.000491	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.776
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.282
• ghis: 0.502

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc1

Gene ontology

• Biological process: protein folding
• Cellular component: peroxisomal membrane;cytosol
• Molecular function: protein binding;unfolded protein binding