INTS15

protein-coding

integrator complex subunit 15

Gene summary

Involved in RNA polymerase II transcription initiation surveillance and regulation of transcription elongation by RNA polymerase II. Part of INTAC complex and integrator complex. Is active in chromosome and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C7orf26

MANE transcript

NM_024067.4

Inheritance

—

ClinVar variants

U:18B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr7:6,590,021-6,608,726

External References & Databases

Ensembl (ENSG00000146576)

Transcript & Mutation Effects

hg38 • Region Span ~18.7 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 INTS15 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 9

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024067.4. 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			1 clinvar	2 clinvar		3
missense			11 clinvar			11
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	18	2	0	20

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024067.4	RefSeq	NP_076972.2	6	MANE Select
ENST00000344417.10	Ensembl	ENSP00000340220.5	6	MANE Select
NM_001303039.2	RefSeq	NP_001289968.1	7	Standard
ENST00000359073.10	Ensembl	ENSP00000351974.5	7	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344417
Coding exons: 6
Length: 18710
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125746
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.572	296	270	1.10	0.0000166	2875
Missense (PolyPhen)		33	29.77	1.1085		306
Synonymous	-0.798	144	132	1.09	0.00000928	935
Loss of Function	3.47	1	15.9	0.0628	7.38e-7	200

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000054	rare
Finnish	0.000069	0.000046	rare
European (Non-Finnish)	0.000028	0.000026	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.139
RVIS EVS: -0.34
RVIS percentile EVS: 30.56

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): H

Gene Damage Prediction

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