INTS13

integrator complex subunit 13, the group of Integrator complex

Basic information

Region (hg38): 12:26905180-26938326

Previous symbols: [ "C12orf11", "ASUN" ]

Links

ENSG00000064102 ∙ NCBI:55726 ∙ OMIM:615079 ∙ HGNC:20174 ∙ Uniprot:Q9NVM9 ∙ 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 INTS13 gene.

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS13 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	5	0	0

Variants in INTS13

This is a list of pathogenic ClinVar variants found in the INTS13 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-26905519-T-C		not specified	Uncertain significance (Aug 18, 2021)
12-26905535-T-A		not specified	Uncertain significance (May 25, 2022)
12-26906359-C-A		not specified	Uncertain significance (Nov 10, 2022)
12-26906424-T-A		not specified	Uncertain significance (Jan 22, 2024)
12-26906435-G-A		not specified	Uncertain significance (Feb 17, 2022)
12-26911217-C-T		not specified	Uncertain significance (Jan 26, 2022)
12-26914059-T-C		not specified	Uncertain significance (Jul 09, 2021)
12-26914409-G-A		not specified	Uncertain significance (Jan 31, 2022)
12-26914485-C-T		not specified	Uncertain significance (Dec 16, 2023)
12-26914514-T-C		not specified	Uncertain significance (Oct 21, 2021)
12-26917727-G-A		not specified	Uncertain significance (Sep 12, 2023)
12-26917728-A-T		not specified	Likely benign (Sep 29, 2023)
12-26924432-G-C		not specified	Uncertain significance (Mar 07, 2023)
12-26924446-C-A		not specified	Uncertain significance (Oct 27, 2021)
12-26924447-G-A		not specified	Uncertain significance (Oct 26, 2021)
12-26925766-T-C		not specified	Uncertain significance (Jun 05, 2023)
12-26925798-C-A		not specified	Uncertain significance (Mar 11, 2022)
12-26925858-GA-G			Benign (May 14, 2018)
12-26928773-T-G		not specified	Uncertain significance (Dec 16, 2023)
12-26928776-G-A		not specified	Uncertain significance (Jan 11, 2023)
12-26928859-T-G		not specified	Uncertain significance (Jul 05, 2023)
12-26934629-A-G		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS13	protein_coding	protein_coding	ENST00000261191	16	33146

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.862	0.138	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.76	232	384	0.604	0.0000202	4649
Missense in Polyphen		57	124.47	0.45794		1537
Synonymous	-0.207	129	126	1.02	0.00000634	1290
Loss of Function	4.84	8	41.7	0.192	0.00000249	498

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000908	0.0000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Crucial regulator of the mitotic cell cycle and development. At prophase, required for dynein anchoring to the nuclear envelope important for proper centrosome-nucleus coupling. At G2/M phase, may be required for proper spindle formation and execution of cytokinesis. Probable component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing (PubMed:23904267). {ECO:0000269|PubMed:15737938, ECO:0000269|PubMed:23097494, ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:23097494, ECO:0000305|PubMed:23904267}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0908

Intolerance Scores

• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.642
• hipred: Y
• hipred_score: 0.728
• ghis: 0.625

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Ints13

Gene ontology

• Biological process: mitotic spindle organization;regulation of mitotic cell cycle;flagellated sperm motility;snRNA transcription by RNA polymerase II;cell division;centrosome localization;regulation of fertilization;protein localization to nuclear envelope
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: protein binding