TTC4

tetratricopeptide repeat domain 4, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 1:54715860-54742657

Links

ENSG00000243725 ∙ NCBI:7268 ∙ OMIM:606753 ∙ HGNC:12394 ∙ Uniprot:O95801 ∙ 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 TTC4 gene.

• Inborn genetic diseases (8 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC4 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in TTC4

This is a list of pathogenic ClinVar variants found in the TTC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-54715927-G-A		not specified	Uncertain significance (Apr 25, 2022)
1-54715996-T-A		not specified	Uncertain significance (Jun 24, 2022)
1-54716011-T-C		not specified	Uncertain significance (Aug 19, 2023)
1-54717495-A-G		not specified	Uncertain significance (Jan 08, 2024)
1-54717597-A-G		not specified	Uncertain significance (Sep 29, 2023)
1-54717639-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-54731487-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-54731490-G-C		not specified	Uncertain significance (Mar 17, 2023)
1-54731583-A-T		not specified	Uncertain significance (May 03, 2023)
1-54731590-T-A		not specified	Uncertain significance (Aug 12, 2022)
1-54731621-A-G		not specified	Uncertain significance (Nov 03, 2023)
1-54731667-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-54733676-A-G			Uncertain significance (Aug 07, 2018)
1-54737582-G-C		not specified	Uncertain significance (May 03, 2023)
1-54741451-G-A		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC4	protein_coding	protein_coding	ENST00000371281	10	26836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000454	0.962	125576	0	171	125747	0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	188	198	0.949	0.00000966	2540
Missense in Polyphen		37	37.196	0.99474		481
Synonymous	0.550	68	74.0	0.919	0.00000355	694
Loss of Function	1.93	12	21.7	0.554	9.97e-7	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00779	0.00708
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.0000481	0.0000462
European (Non-Finnish)	0.000281	0.000273
Middle Eastern	0.000599	0.000598
South Asian	0.000100	0.0000980
Other	0.000505	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.843
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.8

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.503
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc4

Zebrafish Information Network

• Gene name: ttc4
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Molecular function: protein binding