INTS14

protein-coding

integrator complex subunit 14, the group of Integrator complex

Gene summary

Predicted to enable metal ion binding activity. Involved in RNA polymerase II transcription initiation surveillance; regulation of transcription elongation by RNA polymerase II; and snRNA processing. Located in cytoplasm. Part of INTAC complex and integrator complex. Is active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C15orf44
VWA9

MANE transcript

NM_001394796.1

Inheritance

—

ClinVar variants

U:52B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr15:65,578,753-65,611,289

External References & Databases

Ensembl (ENSG00000138614)

Transcript & Mutation Effects

hg38 • Region Span ~32.5 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 INTS14 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 48

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394796.1. 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			1
missense			47 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	52	1	0	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 77 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394796.1	RefSeq	NP_001381725.1	11	MANE Select
ENST00000313182.7	Ensembl	ENSP00000326379.2	11	MANE Select
NM_001136043.4	RefSeq	NP_001129515.1	10	Standard
NM_001207058.4	RefSeq	NP_001193987.2	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
RNA polymerase II transcribes snRNA genes
RNA Polymerase II Transcription

Biological Process

snRNA 3'-end processing
snRNA transcription by RNA polymerase II

Cellular Component

nucleoplasm
integrator complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000420799
Coding exons: 11
Length: 32537
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 44
Defined: 125747
p: 0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	204	253	0.806	0.0000125	3032
Missense (PolyPhen)		41	73.096	0.5609		903
Synonymous	1.28	83	99.2	0.837	0.00000528	898
Loss of Function	2.22	12	23.7	0.507	0.00000128	270

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00019	0.00019	rare
South Asian	0.000067	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable 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. {ECO:0000250|UniProtKB:Q9VPY0}.;

Recessive Scores

pRec: 0.0906

Intolerance Scores

RVIS EVS: -0.47
RVIS percentile EVS: 23.04

Essentials

Essential (gene trap): N