IST1

IST1 factor associated with ESCRT-III, the group of ESCRT-III associated factors

Basic information

Region (hg38): 16:71845996-71931199

Previous symbols: [ "KIAA0174" ]

Links

ENSG00000182149 ∙ NCBI:9798 ∙ OMIM:616434 ∙ HGNC:28977 ∙ Uniprot:P53990 ∙ 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 IST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IST1 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
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	15	3	2

Variants in IST1

This is a list of pathogenic ClinVar variants found in the IST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-71849771-T-C		not specified	Uncertain significance (Apr 22, 2024)
16-71849801-G-A		not specified	Uncertain significance (Feb 05, 2024)
16-71849829-C-T		not specified	Uncertain significance (Jun 03, 2024)
16-71849900-C-A		not specified	Uncertain significance (Apr 23, 2024)
16-71849931-G-T		not specified	Uncertain significance (May 15, 2023)
16-71849999-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-71850060-C-T		not specified	Uncertain significance (Sep 07, 2022)
16-71850065-A-G		not specified	Uncertain significance (Mar 11, 2022)
16-71850066-C-A		not specified	Uncertain significance (Sep 27, 2021)
16-71850098-C-T		not specified	Uncertain significance (Apr 20, 2024)
16-71850111-A-G		not specified	Uncertain significance (Mar 25, 2024)
16-71850116-C-A		not specified	Uncertain significance (Jan 18, 2022)
16-71850162-G-C		not specified	Uncertain significance (Dec 16, 2023)
16-71850243-C-T		not specified	Uncertain significance (Apr 13, 2023)
16-71850285-C-A		not specified	Uncertain significance (Jun 21, 2021)
16-71850330-C-T		not specified	Uncertain significance (Jan 31, 2023)
16-71850399-T-C		not specified	Uncertain significance (Dec 19, 2022)
16-71850425-A-G		not specified	Uncertain significance (Mar 17, 2023)
16-71850439-G-A		not specified	Uncertain significance (Apr 06, 2023)
16-71850479-C-A		not specified	Uncertain significance (Nov 18, 2022)
16-71850489-C-A		not specified	Uncertain significance (Sep 16, 2021)
16-71850504-C-T		not specified	Uncertain significance (May 02, 2024)
16-71850514-G-C		not specified	Uncertain significance (Jun 14, 2023)
16-71850516-G-T		not specified	Uncertain significance (Sep 01, 2021)
16-71850524-G-C		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IST1	protein_coding	protein_coding	ENST00000535424	10	83015

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00465	0.990	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.661	237	210	1.13	0.0000107	2449
Missense in Polyphen		26	50.91	0.51071		626
Synonymous	-2.62	104	75.1	1.39	0.00000360	769
Loss of Function	2.41	7	18.1	0.387	9.23e-7	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000711	0.000381
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000123	0.000114
Middle Eastern	0.000711	0.000381
South Asian	0.0000982	0.0000653
Other	0.000490	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ESCRT-III-like protein involved in specific functions of the ESCRT machinery. Is required for efficient abscission during cytokinesis, but not for HIV-1 budding. The involvement in the MVB pathway is not established. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells (PubMed:19129479, PubMed:19129480). During late anaphase, involved in nuclear envelope reassembly and mitotic spindle disassembly together with the ESCRT-III complex: IST1 acts by mediating the recruitment of SPAST to the nuclear membrane, leading to microtubule severing (PubMed:26040712). Regulates early endosomal tubulation together with the ESCRT-III complex by mediating the recruitment of SPAST (PubMed:23897888). {ECO:0000269|PubMed:19129479, ECO:0000269|PubMed:19129480, ECO:0000269|PubMed:23897888, ECO:0000269|PubMed:26040712}.
• Pathway: Endocytosis - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.712
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ist1

Zebrafish Information Network

• Gene name: ist1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased mobility

Gene ontology

• Biological process: protein localization;abscission;protein transport;viral release from host cell;multivesicular body assembly;neutrophil degranulation;establishment of protein localization;positive regulation of proteolysis;viral capsid secondary envelopment;positive regulation of collateral sprouting;cell division;cytoskeleton-dependent cytokinesis;ESCRT III complex disassembly
• Cellular component: chromatin;extracellular region;nuclear envelope;endoplasmic reticulum-Golgi intermediate compartment;centrosome;cytosol;midbody;azurophil granule lumen;intracellular membrane-bounded organelle;extracellular exosome;Flemming body
• Molecular function: protein binding;protein domain specific binding;protein-containing complex binding;cadherin binding;MIT domain binding