TTC39B

protein-coding

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

Gene summary

Predicted to be involved in several processes, including cholesterol homeostasis; negative regulation of cholesterol storage; and regulation of cholesterol efflux. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf52

MANE transcript

NM_152574.3

Inheritance

—

ClinVar variants

U:110B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr9:15,163,622-15,307,360

External References & Databases

Ensembl (ENSG00000155158)

Transcript & Mutation Effects

hg38 • Region Span ~143.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TTC39B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152574.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	4 clinvar	5
missense			108 clinvar	5 clinvar	1 clinvar	114
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	110	6	5	121

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152574.3	RefSeq	NP_689787.3	20	MANE Select
ENST00000512701.7	Ensembl	ENSP00000422496.2	20	MANE Select
NM_001168339.2	RefSeq	NP_001161811.2	20	Standard
NM_001168340.2	RefSeq	NP_001161812.2	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lipid metabolic process
regulation of cholesterol efflux
negative regulation of cholesterol storage
cholesterol homeostasis
regulation of cholesterol metabolic process

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000512701
Coding exons: 20
Length: 143739
Individuals with no LoFs: 125597
Homozygous LoFs: 0
Heterozygous LoFs: 151
Defined: 125748
p: 0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.30	417	349	1.20	0.0000177	4429
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00063	0.00062	rare
Latino/Admixed American	0.00083	0.00081	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00044	0.00044	rare
Finnish	0.00046	0.00046	rare
European (Non-Finnish)	0.00070	0.00069	rare
South Asian	0.00020	0.00020	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.744

Gene Damage Prediction

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