TTC7B

protein-coding

tetratricopeptide repeat domain 7B, the group of PI4KA lipid kinase complex|Tetratricopeptide repeat domain containing

Gene summary

Involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TTC7L1

MANE transcript

NM_001010854.2

Inheritance

—

ClinVar variants

U:130B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr14:90,524,564-90,816,479

External References & Databases

Ensembl (ENSG00000165914)

Transcript & Mutation Effects

hg38 • Region Span ~291.9 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 TTC7B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 121

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001010854.2. 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			2 clinvar	2 clinvar	1 clinvar	5
missense			123 clinvar		1 clinvar	124
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	130	2	2	134

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001010854.2	RefSeq	NP_001010854.1	20	MANE Select
ENST00000328459.11	Ensembl	ENSP00000336127.4	20	MANE Select
NM_001320421.2	RefSeq	NP_001307350.1	19	Standard
NM_001401365.1	RefSeq	NP_001388294.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

phosphatidylinositol phosphorylation
protein localization to plasma membrane

Molecular Function

protein binding

Cellular Component

cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328459
Coding exons: 20
Length: 275892
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125748
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.09	369	501	0.737	0.0000301	5416
Missense (PolyPhen)		79	139.41	0.56666		1657
Synonymous	0.505	198	207	0.955	0.0000132	1726
Loss of Function	5.92	4	48.5	0.0825	0.00000257	544

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane. The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis. In the complex, plays a central role in bridging PI4KA to EFR3B and FAM126A, via direct interactions (PubMed:26571211). {ECO:0000269|PubMed:23229899, ECO:0000269|PubMed:26571211}.;

Intolerance Scores

LoFtool: 0.178
RVIS EVS: -1.57
RVIS percentile EVS: 3.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.225

Gene Damage Prediction

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