TIPIN

TIMELESS interacting protein, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 15:66336191-66386746

Links

ENSG00000075131

∙ NCBI:54962 ∙ OMIM:610716 ∙ HGNC:30750 ∙ Uniprot:Q9BVW5 ∙ 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 TIPIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TIPIN gene is commonly pathogenic or not. These statistics are base on trasncript: . Only rare variants are included in the table.

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			14 clinvar			14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TIPIN	protein_coding	protein_coding	ENST00000261881	7	50541

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000160	0.887	125712	0	34	125746	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.300	140	150	0.931	0.00000677	1996
Missense in Polyphen		33	36.167	0.91244		526
Synonymous	0.175	54	55.7	0.970	0.00000275	544
Loss of Function	1.44	8	13.8	0.580	7.42e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000274
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays an important role in the control of DNA replication and the maintenance of replication fork stability. Important for cell survival after DNA damage or replication stress. May be specifically required for the ATR-CHEK1 pathway in the replication checkpoint induced by hydroxyurea or ultraviolet light. Forms a complex with TIMELESS and this complex regulates DNA replication processes under both normal and stress conditions, stabilizes replication forks and influences both CHEK1 phosphorylation and the intra-S phase checkpoint in response to genotoxic stress. {ECO:0000269|PubMed:17102137, ECO:0000269|PubMed:17116885, ECO:0000269|PubMed:17296725}.;
Pathway: HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;DNA Double-Strand Break Repair;Homology Directed Repair;Processing of DNA double-strand break ends;ATR signaling pathway (Consensus)

Recessive Scores

pRec: 0.0868

Intolerance Scores

loftool: 0.800
rvis_EVS: 0.73
rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

pHI: 0.801
hipred: Y
hipred_score: 0.627
ghis: 0.534

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.968

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tipin
Phenotype

Gene ontology

Biological process: DNA replication checkpoint;positive regulation of cell population proliferation;response to UV;intra-S DNA damage checkpoint;regulation of nuclear cell cycle DNA replication;replication fork arrest;cell cycle phase transition;replication fork protection;cell division
Cellular component: nuclear chromatin;nucleus;nucleoplasm;cytoplasm;replication fork protection complex;intracellular membrane-bounded organelle
Molecular function: DNA binding;protein binding