INTS6

integrator complex subunit 6, the group of Integrator complex

Basic information

Region (hg38): 13:51354077-51454264

Previous symbols: [ "DDX26" ]

Links

ENSG00000102786 ∙ NCBI:26512 ∙ OMIM:604331 ∙ HGNC:14879 ∙ Uniprot:Q9UL03 ∙ 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 INTS6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS6 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			31		1	32
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding			2			2
Total	0	0	36	0	1

Variants in INTS6

This is a list of pathogenic ClinVar variants found in the INTS6 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-51355075-G-A		not specified	Uncertain significance (May 25, 2022)
13-51355092-G-A		not specified	Uncertain significance (May 13, 2024)
13-51355099-C-G		not specified	Uncertain significance (Feb 27, 2023)
13-51361828-G-C		not specified	Uncertain significance (Nov 09, 2023)
13-51361834-G-A		not specified	Uncertain significance (Jan 16, 2025)
13-51361858-G-A		not specified	Uncertain significance (Dec 07, 2021)
13-51365759-C-A		not specified	Uncertain significance (Mar 08, 2025)
13-51365759-C-T		not specified	Uncertain significance (Dec 14, 2021)
13-51365824-T-C		not specified	Uncertain significance (Mar 16, 2024)
13-51367807-T-C		INTS6-related disorder	Benign (Apr 11, 2019)
13-51367840-T-C		INTS6-related disorder	Likely benign (Jul 30, 2019)
13-51367868-T-C		not specified	Uncertain significance (Nov 30, 2022)
13-51367869-G-A		not specified	Uncertain significance (Dec 14, 2023)
13-51368993-C-G		not specified	Uncertain significance (Oct 04, 2023)
13-51369005-T-G		not specified	Uncertain significance (Nov 05, 2021)
13-51369022-T-C		not specified	Uncertain significance (Feb 19, 2025)
13-51369025-T-C		not specified	Uncertain significance (Nov 10, 2022)
13-51369056-T-C		not specified	Uncertain significance (Nov 10, 2022)
13-51369088-T-G		not specified	Uncertain significance (Oct 12, 2021)
13-51369166-T-C		not specified	Uncertain significance (Mar 14, 2023)
13-51369170-T-C			Benign (Apr 04, 2018)
13-51369176-G-A		not specified	Uncertain significance (Feb 16, 2023)
13-51369191-C-T		not specified	Uncertain significance (Jan 31, 2025)
13-51369202-G-C		INTS6-related disorder	Likely benign (Feb 19, 2019)
13-51369214-G-A		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS6	protein_coding	protein_coding	ENST00000311234	18	100188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000148	125694	0	4	125698	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.83	233	466	0.500	0.0000228	5822
Missense in Polyphen		55	185.56	0.2964		2461
Synonymous	-1.05	175	158	1.11	0.00000750	1678
Loss of Function	6.03	2	46.3	0.0432	0.00000254	569

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000591	0.0000591
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000554	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000880
Middle Eastern	0.0000554	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). May have a tumor suppressor role; an ectopic expression suppressing tumor cell growth (PubMed:15254679, PubMed:16239144). {ECO:0000269|PubMed:15254679, ECO:0000269|PubMed:16239144, ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.0140
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.73

Haploinsufficiency Scores

• pHI: 0.333
• hipred: Y
• hipred_score: 0.783
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.614

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints6
• 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)

Zebrafish Information Network

• Gene name: ints6
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: radial symmetry

Gene ontology

• Biological process: snRNA processing;snRNA 3'-end processing;snRNA transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;actin cytoskeleton;integrator complex
• Molecular function: transmembrane signaling receptor activity;protein binding