STIP1

stress induced phosphoprotein 1, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 11:64185271-64204543

Links

ENSG00000168439 ∙ NCBI:10963 ∙ OMIM:605063 ∙ HGNC:11387 ∙ Uniprot:P31948 ∙ 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 STIP1 gene.

• Inborn genetic diseases (9 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STIP1 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				1	1	2
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in STIP1

This is a list of pathogenic ClinVar variants found in the STIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64193084-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-64193128-C-T			Benign (Jul 06, 2018)
11-64193149-C-T			Benign/Likely benign (Jul 01, 2022)
11-64193152-C-T		not specified	Likely benign (Nov 03, 2023)
11-64194312-A-G		not specified	Uncertain significance (Mar 29, 2022)
11-64194488-T-G		not specified	Uncertain significance (Nov 09, 2023)
11-64194619-A-T		not specified	Uncertain significance (Oct 05, 2023)
11-64195751-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-64197334-A-C		not specified	Uncertain significance (Apr 25, 2022)
11-64197394-G-A		not specified	Uncertain significance (Jan 30, 2024)
11-64197519-A-G		not specified	Uncertain significance (Sep 17, 2021)
11-64197520-A-G		not specified	Uncertain significance (May 23, 2023)
11-64197859-A-G		not specified	Uncertain significance (Feb 28, 2024)
11-64197921-A-T		not specified	Uncertain significance (Oct 10, 2023)
11-64199968-G-A		not specified	Uncertain significance (Dec 20, 2021)
11-64199997-T-A		not specified	Uncertain significance (Nov 03, 2023)
11-64200026-T-G		not specified	Uncertain significance (Oct 06, 2022)
11-64200035-A-C		not specified	Uncertain significance (Sep 15, 2021)
11-64203170-A-G		not specified	Uncertain significance (Jan 24, 2024)
11-64203501-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-64203537-G-A		not specified	Uncertain significance (Jan 19, 2024)
11-64203601-A-G		not specified	Uncertain significance (Jan 03, 2024)
11-64204062-A-G		not specified	Uncertain significance (Nov 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STIP1	protein_coding	protein_coding	ENST00000305218	14	19272

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000135	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	223	320	0.698	0.0000182	3605
Missense in Polyphen		40	96.937	0.41264		1096
Synonymous	-1.14	136	120	1.13	0.00000706	957
Loss of Function	5.31	3	38.6	0.0777	0.00000256	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
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	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a co-chaperone for HSP90AA1 (PubMed:27353360). Mediates the association of the molecular chaperones HSPA8/HSC70 and HSP90 (By similarity). {ECO:0000250|UniProtKB:O35814, ECO:0000303|PubMed:27353360}.
• Pathway: Prion diseases - Homo sapiens (human);HSP90 chaperone cycle for steroid hormone receptors (SHR);Cellular responses to stress;Cellular responses to external stimuli;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.188

Intolerance Scores

• loftool: 0.354
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.651
• hipred: Y
• hipred_score: 0.729
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stip1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: cellular response to interleukin-7
• Cellular component: nucleus;Golgi apparatus;cytosol;protein-containing complex;myelin sheath;chaperone complex
• Molecular function: RNA binding;protein binding;protein C-terminus binding;Hsp70 protein binding;chaperone binding;Hsp90 protein binding