TTC39A

tetratricopeptide repeat domain 39A, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 1:51287257-51345116

Previous symbols: [ "C1orf34" ]

Links

ENSG00000085831 ∙ NCBI:22996 ∙ OMIM:619885 ∙ HGNC:18657 ∙ Uniprot:Q5SRH9 ∙ 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 TTC39A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC39A 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in TTC39A

This is a list of pathogenic ClinVar variants found in the TTC39A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-51288180-T-C		not specified	Uncertain significance (Sep 27, 2022)
1-51288188-C-T		not specified	Likely benign (May 27, 2022)
1-51288857-T-C		not specified	Uncertain significance (Jan 31, 2024)
1-51288879-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-51290008-G-C		Wolff-Parkinson-White pattern	Uncertain significance (Jul 14, 2017)
1-51290019-C-A		not specified	Uncertain significance (Oct 26, 2021)
1-51290097-G-C		not specified	Uncertain significance (May 06, 2022)
1-51290532-T-A		not specified	Uncertain significance (Sep 12, 2023)
1-51290556-C-G		not specified	Uncertain significance (Jun 06, 2023)
1-51290570-G-A		Wolff-Parkinson-White pattern	Uncertain significance (Jul 14, 2017)
1-51290589-C-T		not specified	Uncertain significance (Apr 28, 2022)
1-51290595-C-T		not specified	Uncertain significance (May 10, 2024)
1-51294484-A-C		not specified	Uncertain significance (Feb 17, 2022)
1-51301603-T-A		not specified	Uncertain significance (May 26, 2022)
1-51301604-C-T		not specified	Uncertain significance (Feb 11, 2022)
1-51301697-G-C		not specified	Uncertain significance (Oct 26, 2022)
1-51301724-G-A		not specified	Uncertain significance (Aug 04, 2022)
1-51302516-C-T		not specified	Uncertain significance (May 28, 2024)
1-51302517-G-A		not specified	Uncertain significance (Aug 20, 2023)
1-51303144-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-51305090-T-C			Likely benign (Mar 01, 2023)
1-51306065-C-A		not specified	Uncertain significance (Feb 06, 2023)
1-51312849-C-T		not specified	Uncertain significance (Oct 12, 2022)
1-51321821-G-A		not specified	Likely benign (Jul 14, 2023)
1-51345012-G-A		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC39A	protein_coding	protein_coding	ENST00000413473	18	57859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000630	0.999	124605	0	46	124651	0.000185

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.28	203	317	0.640	0.0000173	3784
Missense in Polyphen		59	119.51	0.49367		1431
Synonymous	0.951	117	131	0.894	0.00000790	1048
Loss of Function	3.58	12	34.8	0.345	0.00000160	425

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000224	0.000223
Ashkenazi Jewish	0.000895	0.000895
East Asian	0.000224	0.000223
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000163	0.000159
Middle Eastern	0.000224	0.000223
South Asian	0.000230	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.821
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.303
• hipred: Y
• hipred_score: 0.554
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc39a

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function