TTC7B

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

Basic information

Region (hg38): 14:90524563-90816479

Previous symbols: [ "TTC7L1" ]

Links

ENSG00000165914 ∙ NCBI:145567 ∙ OMIM:620060 ∙ HGNC:19858 ∙ Uniprot:Q86TV6 ∙ 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 TTC7B gene.

• Inborn genetic diseases (36 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC7B 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	2
missense			36		1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	36	1	2

Variants in TTC7B

This is a list of pathogenic ClinVar variants found in the TTC7B region.

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

Position	Type	Phenotype	Significance	ClinVar
14-90541454-C-A		not specified	Uncertain significance (Nov 12, 2021)
14-90541538-G-A		not specified	Uncertain significance (Aug 30, 2022)
14-90541559-T-G		not specified	Uncertain significance (Feb 22, 2023)
14-90578168-G-A		not specified	Uncertain significance (Oct 12, 2023)
14-90578174-C-T		not specified	Uncertain significance (Sep 22, 2022)
14-90578189-G-A		not specified	Uncertain significance (Sep 12, 2023)
14-90578192-G-T			Benign (Dec 13, 2018)
14-90578260-G-C		not specified	Uncertain significance (Apr 28, 2022)
14-90593517-C-A		not specified	Uncertain significance (Aug 04, 2021)
14-90593522-G-A		not specified	Uncertain significance (Jul 31, 2023)
14-90593621-C-T		not specified	Uncertain significance (Feb 15, 2023)
14-90610812-T-G		not specified	Uncertain significance (May 27, 2022)
14-90610828-C-T		not specified	Uncertain significance (May 02, 2023)
14-90617943-G-T		not specified	Uncertain significance (Apr 26, 2023)
14-90618007-C-T		not specified	Uncertain significance (Jul 05, 2023)
14-90618037-A-G		not specified	Uncertain significance (Jun 23, 2023)
14-90644073-G-C		not specified	Uncertain significance (Jul 19, 2022)
14-90644082-C-T		not specified	Uncertain significance (Sep 09, 2021)
14-90644085-T-C		not specified	Uncertain significance (Jul 09, 2021)
14-90644198-G-C		not specified	Uncertain significance (Mar 01, 2024)
14-90646962-T-C		not specified	Uncertain significance (Sep 14, 2022)
14-90646976-G-C		not specified	Uncertain significance (Aug 23, 2021)
14-90652875-C-T		not specified	Uncertain significance (Feb 15, 2023)
14-90655058-G-A		not specified	Uncertain significance (Apr 26, 2023)
14-90655077-C-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC7B	protein_coding	protein_coding	ENST00000328459	20	275892

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000176	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	369	501	0.737	0.0000301	5416
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.0000910
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.297
• hipred: Y
• hipred_score: 0.728
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc7b

Gene ontology

• Biological process: phosphatidylinositol phosphorylation;protein localization to plasma membrane
• Cellular component: cytosol;plasma membrane
• Molecular function: protein binding