INTS7

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

Basic information

Region (hg38): 1:211940399-212035557

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.

not_specified (85 variants)
INTS7-related_disorder (2 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. These statistics are base on transcript: NM_000015434.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			86 clinvar	1 clinvar		87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	86	1	0

Loading clinvar variants...

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
Phenotype

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