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.

not_specified (64 variants)
not_provided (16 variants)
INTS6-related_disorder (10 variants)
INTS6-associated_neurodevelopmental_disorder (1 variants)
Autism_spectrum_disorder (1 variants)

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. These statistics are base on transcript: NM_000012141.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar	2 clinvar	5
missense		1 clinvar	70 clinvar	1 clinvar	1 clinvar	73
nonsense			7 clinvar			7
start loss						0
frameshift			4 clinvar			4
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	1	89	3	3

Loading clinvar variants...

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