INTS7

integrator complex subunit 7, the group of Armadillo like helical domain containing|Integrator complex

Basic information

Region (hg38): 1:211940398-212035557

Previous symbols: [ "C1orf73" ]

Links

ENSG00000143493 ∙ NCBI:25896 ∙ OMIM:611350 ∙ HGNC:24484 ∙ Uniprot:Q9NVH2 ∙ 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 INTS7 gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS7 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in INTS7

This is a list of pathogenic ClinVar variants found in the INTS7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-211941843-T-C		not specified	Uncertain significance (Jun 02, 2023)
1-211941886-G-C		not specified	Uncertain significance (Jul 12, 2023)
1-211941954-G-A		not specified	Uncertain significance (Dec 14, 2023)
1-211942081-C-G		not specified	Uncertain significance (Feb 06, 2024)
1-211944852-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-211944878-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-211944896-T-G		not specified	Uncertain significance (May 05, 2023)
1-211946614-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-211946686-T-C		INTS7-related disorder	Likely benign (Dec 01, 2022)
1-211967922-C-G		not specified	Uncertain significance (Sep 21, 2023)
1-211967952-G-T		not specified	Uncertain significance (Aug 14, 2023)
1-211967956-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-211968563-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-211968686-G-C		not specified	Uncertain significance (Mar 23, 2022)
1-211975309-A-T		not specified	Uncertain significance (Mar 01, 2023)
1-211976628-G-C		not specified	Uncertain significance (Mar 01, 2023)
1-211976652-A-G		not specified	Uncertain significance (Dec 02, 2022)
1-211978277-G-T		not specified	Uncertain significance (Jan 02, 2024)
1-211978405-C-T		not specified	Uncertain significance (May 30, 2023)
1-211978432-T-G		not specified	Uncertain significance (Feb 02, 2022)
1-211978493-C-T		not specified	Uncertain significance (Dec 19, 2023)
1-211981129-A-C		not specified	Uncertain significance (Nov 03, 2023)
1-211981178-A-G		not specified	Uncertain significance (Mar 20, 2023)
1-211982715-T-C		not specified	Uncertain significance (Nov 08, 2022)
1-211982762-T-C		INTS7-related disorder	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS7	protein_coding	protein_coding	ENST00000366994	20	95144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000126	1.00	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	365	499	0.731	0.0000244	6298
Missense in Polyphen		107	178.85	0.59826		2254
Synonymous	0.454	172	180	0.957	0.00000846	1859
Loss of Function	3.99	17	46.3	0.367	0.00000219	587

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000165	0.000163
South Asian	0.000131	0.000131
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Plays a role in DNA damage response (DDR) signaling during the S phase (PubMed:21659603). May be not involved in the recruitment of cytoplasmic dynein to the nuclear envelope by different components of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:21659603, ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.410
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

• pHI: 0.488
• hipred: Y
• hipred_score: 0.746
• ghis: 0.650

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints7

Zebrafish Information Network

• Gene name: ints7
• Affected structure: neurocranium
• Phenotype tag: abnormal
• Phenotype quality: shape

Gene ontology

• Biological process: DNA damage checkpoint;snRNA processing;snRNA 3'-end processing;snRNA transcription by RNA polymerase II;cellular response to ionizing radiation
• Cellular component: nucleus;nucleoplasm;chromosome;cytoplasm;nuclear body;integrator complex
• Molecular function: protein binding