INTS10

integrator complex subunit 10, the group of Integrator complex

Basic information

Region (hg38): 8:19817390-19852083

Previous symbols: [ "C8orf35" ]

Links

ENSG00000104613 ∙ NCBI:55174 ∙ OMIM:611353 ∙ HGNC:25548 ∙ Uniprot:Q9NVR2 ∙ 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 INTS10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS10 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	0

Variants in INTS10

This is a list of pathogenic ClinVar variants found in the INTS10 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-19817548-A-G		not specified	Uncertain significance (Feb 07, 2023)
8-19817568-G-T		not specified	Uncertain significance (Jan 09, 2024)
8-19817611-C-G		not specified	Uncertain significance (Oct 27, 2023)
8-19817638-G-T		not specified	Uncertain significance (Nov 18, 2023)
8-19818297-G-A		not specified	Uncertain significance (Dec 21, 2021)
8-19820390-A-G		not specified	Uncertain significance (Dec 21, 2022)
8-19820393-C-T		not specified	Uncertain significance (Dec 03, 2021)
8-19820502-C-T		not specified	Uncertain significance (Jul 12, 2023)
8-19822451-G-A		not specified	Uncertain significance (Dec 19, 2023)
8-19823303-T-G		not specified	Uncertain significance (Nov 05, 2021)
8-19823304-G-T		not specified	Uncertain significance (Dec 07, 2021)
8-19823354-A-C		not specified	Uncertain significance (Aug 12, 2021)
8-19823381-G-A		not specified	Uncertain significance (Nov 09, 2021)
8-19823892-T-A		not specified	Uncertain significance (Oct 04, 2022)
8-19823945-C-T		not specified	Uncertain significance (Jul 12, 2023)
8-19823965-G-A		not specified	Uncertain significance (Jan 31, 2022)
8-19824925-A-G		not specified	Uncertain significance (Jun 06, 2023)
8-19826504-G-A		not specified	Uncertain significance (Feb 15, 2023)
8-19826557-A-G		not specified	Uncertain significance (Dec 06, 2023)
8-19830428-C-G		not specified	Uncertain significance (Oct 04, 2022)
8-19830489-A-T		not specified	Uncertain significance (Feb 22, 2023)
8-19830536-A-G		not specified	Uncertain significance (Jan 31, 2022)
8-19832086-C-A		not specified	Uncertain significance (Feb 14, 2023)
8-19833185-C-T		not specified	Uncertain significance (Dec 06, 2022)
8-19833211-G-A		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS10	protein_coding	protein_coding	ENST00000397977	17	34944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000141	124765	0	35	124800	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	312	392	0.795	0.0000208	4695
Missense in Polyphen		51	82.192	0.6205		969
Synonymous	-0.308	158	153	1.03	0.00000875	1287
Loss of Function	5.59	2	40.2	0.0497	0.00000184	503

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.00141	0.00134
Finnish	0.00	0.00
European (Non-Finnish)	0.0000364	0.0000353
Middle Eastern	0.00141	0.00134
South Asian	0.000198	0.000196
Other	0.00	0.00

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). 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:23904267, ECO:0000305|PubMed:16239144}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.125
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.119
• hipred: Y
• hipred_score: 0.736
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.896

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints10

Gene ontology

• Biological process: snRNA processing;snRNA transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;integrator complex
• Molecular function: protein binding