INTS6L

protein-coding

integrator complex subunit 6 like, the group of Integrator complex

Gene summary

Predicted to enable protein-macromolecule adaptor activity. Predicted to be involved in snRNA 3'-end processing. Located in centrosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

DDX26B

MANE transcript

NM_001351601.3

Inheritance

—

ClinVar variants

U:150B:3

Top phenotype

Oromandibular-limb hypogenesis spectrum

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chrX:135,520,659-135,582,510

External References & Databases

Ensembl (ENSG00000165359)

Transcript & Mutation Effects

hg38 • Region Span ~61.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to INTS6L variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 6

not providedTotal: 4

Oromandibular-limb hypogenesis spectrumTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001351601.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			27 clinvar	1 clinvar		28
missense			89 clinvar	2 clinvar		91
nonsense			14 clinvar			14
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			19 clinvar			19
Total	0	0	150	3	0	153

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001351601.3	RefSeq	NP_001338530.1	18	MANE Select
ENST00000639893.2	Ensembl	ENSP00000491427.1	18	MANE Select
NM_001351603.3	RefSeq	NP_001338532.1	18	Standard
NM_001351604.3	RefSeq	NP_001338533.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

snRNA 3'-end processing

Cellular Component

integrator complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370752
Coding exons: 17
Length: 61852
Individuals with no LoFs: 125731
Homozygous LoFs: 3
Heterozygous LoFs: 4
Defined: 125738
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.71	217	300	0.723	0.0000213	5614
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000073	0.000058	rare
Ashkenazi Jewish	0.00013	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000056	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0957

Intolerance Scores

RVIS EVS: -0.07
RVIS percentile EVS: 48.69

Essentials

Essential (gene trap): N