INTS6L

integrator complex subunit 6 like, the group of Integrator complex

Basic information

Region (hg38): X:135520659-135582510

Previous symbols: [ "DDX26B" ]

Links

ENSG00000165359 ∙ NCBI:203522 ∙ ∙ HGNC:27334 ∙ Uniprot:Q5JSJ4 ∙ 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 INTS6L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS6L 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			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	2	0

Variants in INTS6L

This is a list of pathogenic ClinVar variants found in the INTS6L region.

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

Position	Type	Phenotype	Significance	ClinVar
X-135546391-AT-A		Oromandibular-limb hypogenesis spectrum	Uncertain significance (Aug 12, 2016)
X-135549715-T-C			Likely benign (Mar 01, 2023)
X-135549726-C-T			Likely benign (Mar 01, 2023)
X-135549729-A-T			Likely benign (Jan 01, 2025)
X-135579806-A-T		not specified	Uncertain significance (Sep 16, 2021)
X-135580052-C-T		not specified	Uncertain significance (Aug 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS6L	protein_coding	protein_coding	ENST00000370752	17	61852

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000819	125731	3	4	125738	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	217	300	0.723	0.0000213	5614
Missense in Polyphen		84	133.54	0.62903		2563
Synonymous	-0.138	111	109	1.02	0.00000786	1676
Loss of Function	5.00	1	31.1	0.0321	0.00000259	538

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000729	0.0000729
Ashkenazi Jewish	0.000135	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000563	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0957

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.69

Haploinsufficiency Scores

• pHI: 0.478
• hipred: Y
• hipred_score: 0.572
• ghis: 0.542

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ints6l

Gene ontology

• Biological process: snRNA 3'-end processing
• Cellular component: integrator complex