TTC24

tetratricopeptide repeat domain 24, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 1:156579722-156587719

Links

ENSG00000187862 ∙ NCBI:164118 ∙ ∙ HGNC:32348 ∙ Uniprot:A2A3L6 ∙ 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 TTC24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC24 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				1		1
missense			45	4		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	5	0

Variants in TTC24

This is a list of pathogenic ClinVar variants found in the TTC24 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156581440-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-156581455-C-T		not specified	Uncertain significance (May 17, 2023)
1-156581469-C-A		not specified	Uncertain significance (Mar 20, 2024)
1-156581476-G-A		not specified	Uncertain significance (Jul 12, 2022)
1-156581482-A-C		not specified	Uncertain significance (Dec 03, 2021)
1-156581523-T-G		not specified	Uncertain significance (Dec 18, 2023)
1-156581549-C-T		not specified	Uncertain significance (Sep 29, 2022)
1-156581582-G-A		not specified	Uncertain significance (Aug 23, 2021)
1-156581658-C-T			Likely benign (Feb 01, 2023)
1-156581675-G-A		not specified	Likely benign (Jan 19, 2024)
1-156581708-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-156581716-G-A		not specified	Uncertain significance (Sep 22, 2023)
1-156581775-G-T		not specified	Uncertain significance (May 09, 2022)
1-156581791-G-A		not specified	Uncertain significance (Dec 12, 2023)
1-156581824-G-A		not specified	Uncertain significance (Jul 25, 2023)
1-156581860-G-A		not specified	Uncertain significance (Jul 05, 2022)
1-156581878-C-G		not specified	Uncertain significance (Feb 28, 2023)
1-156581935-C-T		not specified	Uncertain significance (May 18, 2023)
1-156581936-G-A		not specified	Likely benign (Apr 13, 2022)
1-156581962-G-A		not specified	Uncertain significance (Jul 19, 2023)
1-156581962-G-T		not specified	Uncertain significance (Jan 31, 2024)
1-156581963-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-156581990-G-A		not specified	Likely benign (Aug 08, 2022)
1-156581995-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-156581996-G-A		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC24	protein_coding	protein_coding	ENST00000368236	10	7044

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-8	0.894	116016	226	8394	124636	0.0352

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.932	263	309	0.851	0.0000170	3694
Missense in Polyphen		87	107.01	0.81305		1290
Synonymous	0.958	118	132	0.894	0.00000759	1207
Loss of Function	1.73	16	25.4	0.630	0.00000134	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.126	0.120
Ashkenazi Jewish	0.0237	0.0214
East Asian	0.0221	0.0207
Finnish	0.0238	0.0229
European (Non-Finnish)	0.0297	0.0280
Middle Eastern	0.0221	0.0207
South Asian	0.0783	0.0730
Other	0.0347	0.0315

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.703
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.36

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc24