TTC39B

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

Basic information

Region (hg38): 9:15163621-15307360

Previous symbols: [ "C9orf52" ]

Links

ENSG00000155158 ∙ NCBI:158219 ∙ OMIM:613574 ∙ HGNC:23704 ∙ Uniprot:Q5VTQ0 ∙ 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 TTC39B gene.

• Inborn genetic diseases (37 variants)
• not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC39B 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	4	5
missense			34	2	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			2		2	4
Total	0	0	36	3	7

Variants in TTC39B

This is a list of pathogenic ClinVar variants found in the TTC39B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-15175041-T-C			Benign (Dec 31, 2019)
9-15175066-T-A		not specified	Uncertain significance (Nov 08, 2022)
9-15175071-A-G		not specified	Uncertain significance (Nov 10, 2022)
9-15175100-G-A		not specified	Uncertain significance (Nov 15, 2021)
9-15177720-T-C			Benign (May 30, 2018)
9-15177750-C-A		not specified	Uncertain significance (Apr 22, 2022)
9-15182372-C-A		not specified	Uncertain significance (Oct 12, 2021)
9-15182403-C-G		not specified	Uncertain significance (Jan 05, 2022)
9-15185329-C-T		not specified	Uncertain significance (Jun 02, 2023)
9-15185332-C-T		not specified	Uncertain significance (Jul 25, 2023)
9-15185363-G-A		not specified	Uncertain significance (Jan 31, 2022)
9-15186962-T-C		not specified	Uncertain significance (Dec 28, 2022)
9-15186977-A-C		not specified	Uncertain significance (Jun 23, 2023)
9-15186978-C-A		not specified	Uncertain significance (Jun 23, 2023)
9-15186993-G-A		not specified	Uncertain significance (Sep 16, 2021)
9-15187012-T-C			Benign (Apr 30, 2018)
9-15188020-T-C		not specified	Uncertain significance (Feb 07, 2023)
9-15188030-T-A		not specified	Uncertain significance (Feb 01, 2023)
9-15189603-T-C		not specified	Uncertain significance (May 05, 2023)
9-15189609-C-A		not specified	Uncertain significance (May 06, 2022)
9-15189629-G-A		not specified	Uncertain significance (Jun 22, 2023)
9-15189721-G-A			Benign (Apr 30, 2018)
9-15189744-A-G		not specified	Uncertain significance (Jan 06, 2023)
9-15189759-C-T		not specified	Uncertain significance (Jul 20, 2022)
9-15190571-T-A		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC39B	protein_coding	protein_coding	ENST00000512701	20	143739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.18e-15	0.577	125597	0	151	125748	0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.30	417	349	1.20	0.0000177	4429
Missense in Polyphen		154	140.62	1.0951		1818
Synonymous	-2.91	177	134	1.32	0.00000709	1272
Loss of Function	1.69	29	40.6	0.714	0.00000181	525

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00146	0.00145
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000444	0.000435
Finnish	0.000464	0.000462
European (Non-Finnish)	0.000700	0.000695
Middle Eastern	0.000444	0.000435
South Asian	0.000198	0.000196
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates high density lipoprotein (HDL) cholesterol metabolism by promoting the ubiquitination and degradation of the oxysterols receptors LXR (NR1H2 and NR1H3). {ECO:0000250|UniProtKB:Q8BYY4}.

Recessive Scores

• pRec: 0.0885

Intolerance Scores

• loftool: 0.958
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.86

Haploinsufficiency Scores

• pHI: 0.244
• hipred: N
• hipred_score: 0.251
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.744

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc39b
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: lipid metabolic process;regulation of cholesterol efflux;negative regulation of cholesterol storage;cholesterol homeostasis;regulation of cholesterol metabolic process