TULP4

TUB like protein 4, the group of WD repeat domain containing

Basic information

Region (hg38): 6:158232235-158511828

Links

ENSG00000130338 ∙ NCBI:56995 ∙ OMIM:619442 ∙ HGNC:15530 ∙ Uniprot:Q9NRJ4 ∙ 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 TULP4 gene.

• Inborn genetic diseases (88 variants)
• not provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TULP4 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				6	3	9
missense			86	7		93
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	86	13	3

Variants in TULP4

This is a list of pathogenic ClinVar variants found in the TULP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-158314089-C-T		not specified	Uncertain significance (Dec 28, 2023)
6-158314116-C-G		not specified	Uncertain significance (Feb 16, 2023)
6-158314225-C-T		not specified	Uncertain significance (Aug 04, 2023)
6-158314251-C-T		not specified	Uncertain significance (Jan 17, 2024)
6-158314261-A-G		not specified	Uncertain significance (Dec 20, 2022)
6-158314266-G-A		not specified	Uncertain significance (Mar 21, 2023)
6-158413182-C-T		not specified	Uncertain significance (Aug 01, 2022)
6-158429749-C-T		not specified	Uncertain significance (Nov 17, 2022)
6-158429836-C-T		not specified	Uncertain significance (Nov 18, 2022)
6-158429867-G-A			Likely benign (Oct 01, 2022)
6-158449062-G-A		not specified	Uncertain significance (Oct 26, 2022)
6-158449083-G-A		not specified	Uncertain significance (Mar 05, 2024)
6-158449083-G-C		not specified	Uncertain significance (Sep 16, 2021)
6-158449108-A-T		not specified	Uncertain significance (Feb 06, 2023)
6-158452151-C-T		not specified	Uncertain significance (May 03, 2023)
6-158452224-A-G		not specified	Uncertain significance (Aug 12, 2021)
6-158452261-G-A			Likely benign (Mar 01, 2023)
6-158452262-C-A		not specified	Uncertain significance (Dec 13, 2023)
6-158461619-C-T		not specified	Uncertain significance (Nov 12, 2021)
6-158461646-A-G		not specified	Uncertain significance (Jan 29, 2024)
6-158461647-A-G		not specified	Uncertain significance (Dec 14, 2023)
6-158479796-T-C			Likely benign (Mar 01, 2022)
6-158479842-G-A		not specified	Uncertain significance (Jul 27, 2022)
6-158479880-G-A		not specified	Uncertain significance (Dec 12, 2023)
6-158479893-G-A		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TULP4	protein_coding	protein_coding	ENST00000367097	14	199169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.97e-8	125745	0	3	125748	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	844	963	0.876	0.0000619	9987
Missense in Polyphen		324	466.83	0.69404		4813
Synonymous	-3.73	518	421	1.23	0.0000295	3233
Loss of Function	6.72	3	58.5	0.0513	0.00000291	644

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Intolerance Scores

• loftool: 0.110
• rvis_EVS: -2.53
• rvis_percentile_EVS: 0.9

Haploinsufficiency Scores

• pHI: 0.236
• hipred: Y
• hipred_score: 0.768
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.746

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tulp4

Gene ontology

• Biological process: protein ubiquitination;post-translational protein modification;protein localization to cilium
• Cellular component: cytoplasm;cytosol;cilium
• Molecular function: phosphatidylinositol binding