TULP2

protein-coding

TUB like protein 2

Gene summary

TULP2 is a member of a family of tubby-like genes (TULPs) that encode proteins of unknown function. Members of this family have been identified in plants, vertebrates, and invertebrates. The TULP proteins share a conserved C-terminal region of approximately 200 amino acid residues. [provided by RefSeq, Jul 2008]

MANE transcript

NM_003323.3

Inheritance

—

ClinVar variants

U:85B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr19:48,880,965-48,898,744

External References & Databases

Ensembl (ENSG00000104804)

Transcript & Mutation Effects

hg38 • Region Span ~17.8 kb

Loading mutation effect viewer...

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 TULP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003323.3. 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						0
missense			81 clinvar	7 clinvar		88
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	85	7	0	92

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003323.3	RefSeq	NP_003314.2	12	MANE Select
ENST00000221399.8	Ensembl	ENSP00000221399.3	12	MANE Select
ENST00000518572.6	Ensembl	ENSP00000428420.2	11	Standard
ENST00000520977.2	Ensembl	ENSP00000428535.2	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

visual perception
protein localization to cilium
receptor localization to non-motile cilium
protein localization to photoreceptor outer segment

Molecular Function

phosphatidylinositol binding
protein-containing complex binding

Cellular Component

extracellular region
cytoplasm
cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000221399
Coding exons: 12
Length: 17769
Individuals with no LoFs: 125262
Homozygous LoFs: 4
Heterozygous LoFs: 481
Defined: 125747
p: 0.00193

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.526	296	323	0.918	0.0000200	3389
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.025	0.025	notable
Latino/Admixed American	0.00098	0.00095	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00024	0.00023	rare
South Asian	0.00023	0.00023	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.200
RVIS EVS: 1.65
RVIS percentile EVS: 96.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.754

Gene Damage Prediction

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