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.

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			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in TIPIN

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

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

Position	Type	Phenotype	Significance	ClinVar
15-66336974-A-G		not specified	Uncertain significance (Dec 28, 2023)
15-66337016-A-G		not specified	Uncertain significance (Oct 27, 2021)
15-66337049-A-G		not specified	Uncertain significance (Apr 04, 2023)
15-66337055-T-C		not specified	Uncertain significance (Sep 12, 2023)
15-66337167-T-G		not specified	Uncertain significance (Mar 24, 2023)
15-66341266-G-A		not specified	Uncertain significance (Jan 03, 2024)
15-66341288-A-G		not specified	Uncertain significance (Jul 20, 2021)
15-66351536-T-C		not specified	Uncertain significance (Jan 25, 2023)
15-66351568-C-T		not specified	Uncertain significance (Dec 26, 2023)
15-66351600-T-A		not specified	Uncertain significance (Jan 03, 2024)
15-66352824-G-A		not specified	Uncertain significance (Aug 22, 2023)
15-66352839-C-A		not specified	Uncertain significance (Oct 20, 2024)
15-66352845-G-T		not specified	Uncertain significance (Mar 26, 2024)
15-66352898-T-C		not specified	Uncertain significance (Aug 20, 2024)
15-66386581-A-C			Benign (Jun 19, 2018)
15-66386653-A-T			Benign (Jun 14, 2018)
15-66386717-C-T			Benign (Jun 14, 2018)
15-66386730-G-A			Benign (May 01, 2022)

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

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