TULP2

TUB like protein 2

Basic information

Region (hg38): 19:48880965-48898744

Links

ENSG00000104804 ∙ NCBI:7288 ∙ OMIM:602309 ∙ HGNC:12424 ∙ Uniprot:O00295 ∙ 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 TULP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TULP2 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						0
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in TULP2

This is a list of pathogenic ClinVar variants found in the TULP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48881022-T-G		not specified	Uncertain significance (Mar 29, 2022)
19-48881093-C-T		not specified	Uncertain significance (May 27, 2022)
19-48881115-C-T		not specified	Uncertain significance (Mar 26, 2024)
19-48883825-G-T		not specified	Uncertain significance (Jul 26, 2021)
19-48883940-C-T		not specified	Uncertain significance (May 01, 2024)
19-48883943-C-G		not specified	Uncertain significance (Jun 17, 2024)
19-48883963-C-T		not specified	Uncertain significance (May 08, 2024)
19-48883966-G-C		not specified	Uncertain significance (Apr 18, 2023)
19-48883967-C-T		not specified	Uncertain significance (Jun 06, 2023)
19-48883976-T-C		not specified	Uncertain significance (Jan 04, 2024)
19-48883979-T-C		not specified	Uncertain significance (Mar 17, 2023)
19-48883990-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-48883991-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-48885470-C-T		not specified	Uncertain significance (Jul 19, 2022)
19-48885478-C-T		not specified	Uncertain significance (May 14, 2024)
19-48885509-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-48885535-C-G		not specified	Uncertain significance (Nov 14, 2023)
19-48885544-C-T		not specified	Uncertain significance (Jul 13, 2022)
19-48887978-A-G		not specified	Uncertain significance (Sep 30, 2022)
19-48888057-G-A		not specified	Uncertain significance (Jul 06, 2022)
19-48888072-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-48888101-G-A		not specified	Uncertain significance (Sep 14, 2022)
19-48888114-G-A		not specified	Uncertain significance (Sep 15, 2021)
19-48888116-A-G		not specified	Uncertain significance (Oct 10, 2023)
19-48888139-C-T		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TULP2	protein_coding	protein_coding	ENST00000221399	12	17769

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.47e-16	0.0597	125262	4	481	125747	0.00193

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.526	296	323	0.918	0.0000200	3389
Missense in Polyphen		98	99.263	0.98727		1137
Synonymous	0.320	132	137	0.965	0.00000903	1032
Loss of Function	0.826	27	32.0	0.842	0.00000213	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0261	0.0261
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000239	0.000229
Middle Eastern	0.000435	0.000435
South Asian	0.000229	0.000229
Other	0.00132	0.00130

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.200
• rvis_EVS: 1.65
• rvis_percentile_EVS: 96.18

Haploinsufficiency Scores

• pHI: 0.0745
• hipred: N
• hipred_score: 0.172

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.754

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tulp2

Gene ontology

• Biological process: visual perception;protein localization to cilium;receptor localization to non-motile cilium;protein localization to photoreceptor outer segment
• Cellular component: extracellular region;cytoplasm;cilium
• Molecular function: phosphatidylinositol binding;protein-containing complex binding