TTC12

tetratricopeptide repeat domain 12, the group of Armadillo like helical domain containing|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 11:113314578-113383544

Links

ENSG00000149292 ∙ NCBI:54970 ∙ OMIM:610732 ∙ HGNC:23700 ∙ Uniprot:Q9H892 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliary dyskinesia, primary, 45 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• ciliary dyskinesia, primary, 45 (Moderate), mode of inheritance: AR
• ciliary dyskinesia, primary, 45 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Primary ciliary dyskinesia 45	AR	Allergy/Immunology/Infectious; Pulmonary	Pulmonary surveillance may be beneficial to assess respiratory function and institute early management measures; In order to facilitate mucus clearance, aggressive interventions (eg, chest percussion and oscillatory vest), as well as vaccinations and early and aggressive treatment of respiratory infections may be beneficial	Allergy/Immunology/Infectious; Genitourinary; Pulmonary	31978331

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TTC12 gene.

• not provided (39 variants)
• Inborn genetic diseases (27 variants)
• Ciliary dyskinesia, primary, 45 (4 variants)
• TTC12-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC12 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				2	1	3
missense			23	3	1	27
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					31	31
Total	1	0	23	5	33

Highest pathogenic variant AF is 0.0000197

Variants in TTC12

This is a list of pathogenic ClinVar variants found in the TTC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-113316054-G-A			Benign (May 15, 2021)
11-113316157-C-T			Benign (May 17, 2021)
11-113316283-T-G		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
11-113323102-CA-C			Benign (May 19, 2021)
11-113323102-C-CA			Benign (Jun 04, 2021)
11-113323114-A-C			Benign (May 19, 2021)
11-113323241-C-G			Benign (May 20, 2021)
11-113323254-T-C			Benign (May 17, 2021)
11-113323284-C-G		TTC12-related disorder	Likely benign (Feb 26, 2024)
11-113323314-G-C		Inborn genetic diseases	Uncertain significance (Aug 21, 2023)
11-113323331-A-T		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
11-113323345-T-C		Inborn genetic diseases	Uncertain significance (Oct 29, 2021)
11-113323363-T-G		Inborn genetic diseases	Uncertain significance (Jun 30, 2022)
11-113323371-A-G		Inborn genetic diseases	Uncertain significance (Jan 05, 2022)
11-113323414-A-G		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
11-113323446-A-C		Ciliary dyskinesia, primary, 45	Benign (Sep 10, 2021)
11-113323597-AT-A			Benign (May 17, 2021)
11-113324643-C-T		Inborn genetic diseases	Pathogenic (Jun 10, 2022)
11-113324873-A-G			Benign (May 15, 2021)
11-113325530-A-G		Inborn genetic diseases	Uncertain significance (Oct 29, 2021)
11-113329836-A-G			Benign (May 16, 2021)
11-113329987-G-A		Ciliary dyskinesia, primary, 45	Benign (Sep 10, 2021)
11-113330009-A-G			Benign (May 22, 2021)
11-113335035-G-A		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
11-113338706-C-G			Benign (May 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC12	protein_coding	protein_coding	ENST00000529221	21	69016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.79e-17	0.167	124730	10	1008	125748	0.00406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0927	382	377	1.01	0.0000197	4622
Missense in Polyphen		88	95.749	0.91907		1164
Synonymous	-0.398	150	144	1.04	0.00000797	1326
Loss of Function	1.31	31	39.9	0.777	0.00000204	495

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0196	0.0196
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.0114	0.0113
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000697	0.000686
Middle Eastern	0.0114	0.0113
South Asian	0.00177	0.00157
Other	0.00294	0.00294

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0969

Intolerance Scores

• loftool: 0.911
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.25

Haploinsufficiency Scores

• pHI: 0.0461
• hipred: N
• hipred_score: 0.303
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.599

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc12

Gene ontology

• Cellular component: centrosome