INTS14

integrator complex subunit 14, the group of Integrator complex

Basic information

Region (hg38): 15:65578753-65611289

Previous symbols: [ "C15orf44", "VWA9" ]

Links

ENSG00000138614 ∙ NCBI:81556 ∙ ∙ HGNC:25372 ∙ Uniprot:Q96SY0 ∙ 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 INTS14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS14 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						0
missense			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7			7
Total	0	0	34	1	0

Variants in INTS14

This is a list of pathogenic ClinVar variants found in the INTS14 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65579427-C-T		not specified	Uncertain significance (Sep 29, 2023)
15-65579451-G-A		not specified	Uncertain significance (Aug 02, 2023)
15-65579462-C-G		not specified	Likely benign (Nov 08, 2022)
15-65579473-C-T		not specified	Uncertain significance (Oct 12, 2021)
15-65579579-C-A		not specified	Uncertain significance (Jan 18, 2022)
15-65579643-C-T		not specified	Uncertain significance (Jun 29, 2023)
15-65584778-C-T		not specified	Uncertain significance (Mar 14, 2023)
15-65584819-C-T		not specified	Uncertain significance (Dec 13, 2022)
15-65584828-T-C		not specified	Uncertain significance (Sep 16, 2021)
15-65591645-T-C		not specified	Uncertain significance (Jul 12, 2022)
15-65591700-C-A		not specified	Uncertain significance (Sep 24, 2024)
15-65591730-G-A		not specified	Uncertain significance (May 17, 2023)
15-65593557-C-T		not specified	Uncertain significance (Feb 06, 2024)
15-65593561-C-T		not specified	Uncertain significance (Apr 20, 2024)
15-65595757-C-G		not specified	Uncertain significance (Apr 14, 2022)
15-65598336-T-C		not specified	Uncertain significance (Dec 21, 2022)
15-65598345-G-C		not specified	Uncertain significance (Oct 01, 2024)
15-65598350-A-G		not specified	Uncertain significance (Dec 07, 2021)
15-65598371-G-T		not specified	Uncertain significance (Jul 10, 2024)
15-65598440-G-A		not specified	Uncertain significance (Sep 28, 2022)
15-65598938-T-C		not specified	Uncertain significance (Dec 10, 2024)
15-65599787-G-A		not specified	Uncertain significance (Jan 26, 2025)
15-65599802-T-C		not specified	Uncertain significance (Dec 31, 2024)
15-65599880-C-T		not specified	Uncertain significance (Oct 01, 2024)
15-65605164-C-T		not specified	Uncertain significance (Aug 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS14	protein_coding	protein_coding	ENST00000420799	11	32537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000983	0.987	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	204	253	0.806	0.0000125	3032
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000187	0.000185
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000218	0.000217
South Asian	0.0000669	0.0000653
Other	0.000164	0.000163

dbNSFP

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}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0906

Intolerance Scores

• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.476
• ghis: 0.641

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ints14

Gene ontology

• Biological process: snRNA 3'-end processing;snRNA transcription by RNA polymerase II
• Cellular component: nucleoplasm;integrator complex