INTS1
Basic information
Region (hg38): 7:1470277-1504389
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies (Moderate), mode of inheritance: AR
- neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 28542170; 30622326; 31428919 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (3 variants)
- Inborn genetic diseases (2 variants)
- Neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS1 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 | 76 | 25 | 102 | |||
missense | 240 | 17 | 262 | |||
nonsense | 5 | |||||
start loss | 0 | |||||
frameshift | 7 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 4 | |||||
splice region | 6 | 10 | 8 | 24 | ||
non coding | 18 | 23 | ||||
Total | 6 | 8 | 245 | 97 | 48 |
Highest pathogenic variant AF is 0.0000132
Variants in INTS1
This is a list of pathogenic ClinVar variants found in the INTS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-1470582-T-G | Uncertain significance (Aug 15, 2022) | |||
7-1470586-GGCCTCCATAT-AGGCTCACATCACG | Inborn genetic diseases | Uncertain significance (Feb 25, 2022) | ||
7-1470588-C-G | Inborn genetic diseases | Uncertain significance (Jan 19, 2022) | ||
7-1470594-T-C | Inborn genetic diseases | Uncertain significance (Jan 19, 2022) | ||
7-1470627-C-T | Inborn genetic diseases | Uncertain significance (Jan 06, 2022) | ||
7-1470645-C-T | Inborn genetic diseases | Uncertain significance (Feb 11, 2022) | ||
7-1470651-T-C | Uncertain significance (Nov 30, 2021) | |||
7-1470686-G-A | Uncertain significance (May 18, 2023) | |||
7-1470687-C-T | Inborn genetic diseases | Uncertain significance (Nov 08, 2022) | ||
7-1470849-G-C | Uncertain significance (May 30, 2019) | |||
7-1470858-G-C | Inborn genetic diseases | Uncertain significance (Jun 03, 2022) | ||
7-1470874-G-T | Inborn genetic diseases | Uncertain significance (Jul 13, 2021) | ||
7-1470876-T-G | Inborn genetic diseases | Uncertain significance (Jun 07, 2024) | ||
7-1470887-G-A | Inborn genetic diseases | Uncertain significance (Dec 11, 2023) | ||
7-1470922-G-C | Pathogenic (Dec 19, 2019) | |||
7-1470931-C-T | INTS1-related disorder | Likely benign (Mar 01, 2019) | ||
7-1470934-G-A | INTS1-related disorder | Likely benign (Jun 18, 2019) | ||
7-1471160-G-A | Neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies | Uncertain significance (Mar 29, 2024) | ||
7-1471173-C-T | Inborn genetic diseases | Uncertain significance (Nov 17, 2022) | ||
7-1471181-C-T | Inborn genetic diseases | Uncertain significance (May 20, 2024) | ||
7-1471184-C-A | Inborn genetic diseases | Uncertain significance (Oct 13, 2023) | ||
7-1471195-G-A | Benign (Dec 31, 2019) | |||
7-1471198-C-T | Benign (Jun 01, 2024) | |||
7-1471212-G-A | Inborn genetic diseases | Uncertain significance (Jan 17, 2024) | ||
7-1471218-G-A | Likely benign (Mar 01, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
INTS1 | protein_coding | protein_coding | ENST00000404767 | 47 | 35577 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
7.11e-11 | 1.00 | 124565 | 0 | 148 | 124713 | 0.000594 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.41 | 1208 | 1.35e+3 | 0.892 | 0.0000930 | 13930 |
Missense in Polyphen | 210 | 293.53 | 0.71544 | 2984 | ||
Synonymous | -6.22 | 828 | 629 | 1.32 | 0.0000476 | 4510 |
Loss of Function | 5.98 | 37 | 102 | 0.362 | 0.00000507 | 1111 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00113 | 0.00109 |
Ashkenazi Jewish | 0.000200 | 0.000199 |
East Asian | 0.000622 | 0.000612 |
Finnish | 0.000589 | 0.000557 |
European (Non-Finnish) | 0.000751 | 0.000717 |
Middle Eastern | 0.000622 | 0.000612 |
South Asian | 0.000367 | 0.000360 |
Other | 0.000675 | 0.000660 |
dbNSFP
Source:
- 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). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component 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)
Intolerance Scores
- loftool
- 0.589
- rvis_EVS
- -5.05
- rvis_percentile_EVS
- 0.07
Haploinsufficiency Scores
- pHI
- 0.156
- hipred
- Y
- hipred_score
- 0.648
- ghis
- 0.645
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ints1
- Phenotype
- embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- snRNA processing;U2 snRNA 3'-end processing;snRNA transcription by RNA polymerase II
- Cellular component
- nucleoplasm;membrane;integral component of membrane;nuclear membrane;integrator complex
- Molecular function