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  3. INTS6
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Intellectual disability

Gene: INTS6

Red List (low evidence)
INTS6 (integrator complex subunit 6)
EnsemblGeneIds (GRCh38): ENSG00000102786
EnsemblGeneIds (GRCh37): ENSG00000102786
OMIM: 604331, Gene2Phenotype
INTS6 is in 1 panel

2 reviews

Arina Puzriakova (Genomics England Curator)

Comment on list classification: The Red review by Konstantinos Varvagiannis supports the current Red rating of CPD. There is currently no evidence to support this gene-disease association, and therefore have kept rating as Red.
Created: 28 Sep 2020, 4:01 p.m. | Last Modified: 28 Sep 2020, 4:01 p.m.
Panel Version: 3.355
Created: 28 Sep 2020, 4:01 p.m.
Last Modified: 28 Sep 2020, 4:01 p.m.
Panel version: 3.355

Konstantinos Varvagiannis (Other)

Red List (low evidence)

INTS6 was present in the current panel with red rating, though not previously reviewed.

A search in pubmed (also including alternative names eg. DDX26 or DICE1) did not yield any relevant results, apart from an article on 13q14 deletions in individuals with ID (in all cases >4Mb and spanning several other genes | PMID: 26475974).

There is no associated phenotype in OMIM or G2P.
The gene is not listed in the SysID database.

In SFARI, INTS6 appears to be a strong candidate gene (category 2) for autism (2 individuals with de novo variants and ASD reported - details below, no de novo variants found in SSC unaffected siblings, analysis of combined datasets from the SSC and ASC consortia for ASD suggested enrichment for variants).

The denovo-db lists the same 2 ASD subjects included in SFARI, one with a dn missense variant [NM_012141.2:c.410C>T / p.T137I - PMID: 2536768] and the other with a dn nonsense SNV [NM_012141.2:c.1828C>T / p.R610* - PMID: 25961944]. Both subjects were identified in the context of large patient cohorts. Two further individuals did not have pertinent phenotype.

In Decipher there are no relevant CNVs (spanning only INTS6) or SNVs. The same applies for ClinVar.

INTS6 is not included in gene panels for ID offered by diagnostic laboratories as is also the case with the current ID panel of VCGS (TGW024_genelist_V3 - Oct 2018).

As a result, red rating seems appropriate.
Created: 26 Sep 2019, 5:39 p.m. | Last Modified: 26 Sep 2019, 5:39 p.m.
Panel Version: 2.1046
Created: 26 Sep 2019, 5:39 p.m.
Last Modified: 26 Sep 2019, 5:39 p.m.
Panel version: 2.1046

Details

Sources
  • Expert Review Red
  • Victorian Clinical Genetics Services
OMIM
604331
Clinvar variants
Variants in INTS6
Penetrance
None
Panels with this gene

History Filter Activity

28 Sep 2020, Gel status: 1

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: ints6 has been classified as Red List (Low Evidence).

28 Sep 2018, Gel status: 1

Created, Added New Source, Set mode of inheritance

Louise Daugherty (Genomics England Curator)

gene: INTS6 was added gene: INTS6 was added to Intellectual disability. Sources: Victorian Clinical Genetics Services Mode of inheritance for gene: INTS6 was set to