TTC3

tetratricopeptide repeat domain 3, the group of Tetratricopeptide repeat domain containing|Ring finger proteins

Basic information

Region (hg38): 21:37073225-37203112

Links

ENSG00000182670 ∙ NCBI:7267 ∙ OMIM:602259 ∙ HGNC:12393 ∙ Uniprot:P53804 ∙ 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 TTC3 gene.

• Inborn genetic diseases (94 variants)
• not provided (18 variants)
• Corticobasal syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC3 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				4	7	11
missense			93	4	3	100
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	93	8	11

Variants in TTC3

This is a list of pathogenic ClinVar variants found in the TTC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-37087277-G-A		not specified	Uncertain significance (Feb 28, 2023)
21-37087316-G-A		not specified	Uncertain significance (Feb 05, 2024)
21-37087319-C-G		not specified	Uncertain significance (Jan 23, 2024)
21-37087332-T-C			Likely benign (Aug 01, 2022)
21-37087873-T-C		not specified	Uncertain significance (May 31, 2022)
21-37088213-A-G		not specified	Uncertain significance (May 26, 2023)
21-37088235-C-T		not specified	Uncertain significance (Jun 11, 2021)
21-37088322-G-A		not specified	Uncertain significance (May 10, 2022)
21-37088334-G-A		not specified	Uncertain significance (Oct 20, 2021)
21-37088342-G-A		not specified	Uncertain significance (Dec 01, 2022)
21-37090249-T-C		not specified	Uncertain significance (Jun 23, 2023)
21-37091341-G-A		not specified	Uncertain significance (Jan 07, 2022)
21-37091365-G-A		not specified	Uncertain significance (May 26, 2023)
21-37091369-C-T		not specified	Uncertain significance (Jan 24, 2024)
21-37095344-T-C			Benign (Dec 31, 2019)
21-37095392-A-G		not specified	Uncertain significance (May 18, 2022)
21-37095420-A-G		not specified	Uncertain significance (Jul 28, 2021)
21-37096628-G-C		not specified	Uncertain significance (Dec 05, 2022)
21-37121865-T-C		not specified	Uncertain significance (Feb 16, 2023)
21-37121869-C-T		not specified	Uncertain significance (May 17, 2023)
21-37121904-A-G		not specified	Uncertain significance (Jul 20, 2022)
21-37123001-A-G		not specified	Uncertain significance (May 27, 2022)
21-37124636-G-A		not specified	Likely benign (Aug 11, 2022)
21-37124653-T-C		not specified	Uncertain significance (Jul 19, 2022)
21-37124722-G-A		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC3	protein_coding	protein_coding	ENST00000399017	45	129888

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-40	0.110	125406	2	340	125748	0.00136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.596	978	1.03e+3	0.948	0.0000537	13368
Missense in Polyphen		194	235.83	0.82261		3267
Synonymous	-0.131	365	362	1.01	0.0000199	3633
Loss of Function	2.55	78	106	0.733	0.00000546	1430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00312	0.00309
Ashkenazi Jewish	0.000303	0.000298
East Asian	0.00214	0.00207
Finnish	0.000852	0.000832
European (Non-Finnish)	0.00117	0.00114
Middle Eastern	0.00214	0.00207
South Asian	0.00259	0.00249
Other	0.00116	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that mediates the ubiquitination and subsequent degradation of phosphorylated Akt (AKT1, AKT2 and AKT3) in the nucleus. Acts as a terminal regulator of Akt signaling after activation; its phosphorylation by Akt, which is a prerequisite for ubiquitin ligase activity, suggests the existence of a regulation mechanism required to control Akt levels after activation. Catalyzes the formation of 'Lys-48'- polyubiquitin chains. May play a role in neuronal differentiation inhibition via its interaction with CIT. {ECO:0000269|PubMed:17488780, ECO:0000269|PubMed:20059950}.

Recessive Scores

• pRec: 0.0886

Intolerance Scores

• loftool: 0.992
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.91

Haploinsufficiency Scores

• pHI: 0.336
• hipred: N
• hipred_score: 0.334
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc3

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein K48-linked ubiquitination
• Cellular component: nucleus;nucleolus;cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding;metal ion binding