INTS15

integrator complex subunit 15

Basic information

Region (hg38): 7:6590021-6608726

Previous symbols: [ "C7orf26" ]

Links

ENSG00000146576 ∙ NCBI:79034 ∙ ∙ HGNC:21702 ∙ Uniprot:Q96N11 ∙ 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 INTS15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS15 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				2		2
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in INTS15

This is a list of pathogenic ClinVar variants found in the INTS15 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-6590415-C-G			Likely benign (Mar 01, 2023)
7-6590445-G-A			Likely benign (Nov 01, 2022)
7-6591686-T-C		not specified	Uncertain significance (Oct 12, 2021)
7-6591829-C-G		not specified	Uncertain significance (Oct 22, 2021)
7-6594517-C-T		not specified	Uncertain significance (Sep 17, 2021)
7-6594580-C-T		not specified	Uncertain significance (Oct 22, 2021)
7-6600021-A-G		not specified	Uncertain significance (Nov 09, 2021)
7-6600072-C-T		not specified	Uncertain significance (Aug 13, 2021)
7-6600260-C-T		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS15	protein_coding	protein_coding	ENST00000344417	6	18710

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0235	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.572	296	270	1.10	0.0000166	2875
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000562	0.0000544
Finnish	0.0000692	0.0000462
European (Non-Finnish)	0.0000281	0.0000264
Middle Eastern	0.0000562	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.139
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.595
• ghis: 0.531

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: E130309D02Rik