ATRIP
Basic information
Region (hg38): 3:48446709-48467645
Links
Phenotypes
GenCC
Source:
- Seckel syndrome (Supportive), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (227 variants)
- Aicardi-Goutieres syndrome 1;Chilblain lupus 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (93 variants)
- Aicardi-Goutieres syndrome 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Chilblain lupus 1 (89 variants)
- Aicardi-Goutieres syndrome 1 (59 variants)
- Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Aicardi-Goutieres syndrome 1;Chilblain lupus 1 (49 variants)
- Chilblain lupus 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Aicardi-Goutieres syndrome 1 (39 variants)
- Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (36 variants)
- Inborn genetic diseases (36 variants)
- Chilblain lupus 1;Aicardi-Goutieres syndrome 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (33 variants)
- Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Chilblain lupus 1;Aicardi-Goutieres syndrome 1 (25 variants)
- not specified (16 variants)
- Aicardi Goutieres syndrome (14 variants)
- TREX1-related condition (9 variants)
- TREX1-Related Disorders (4 variants)
- See cases (3 variants)
- Aicardi Goutieres syndrome 1, autosomal dominant (2 variants)
- Aicardi-Goutieres syndrome 1;Systemic lupus erythematosus;Chilblain lupus 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (2 variants)
- Systemic lupus erythematosus (2 variants)
- Aicardi-Goutieres syndrome 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Systemic lupus erythematosus;Chilblain lupus 1 (2 variants)
- Chilblain lupus 1 (2 variants)
- Aicardi-Goutieres syndrome 1;Chilblain lupus 1;Systemic lupus erythematosus;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (1 variants)
- Seckel syndrome (1 variants)
- Neurodevelopmental disorder (1 variants)
- Inborn genetic diseases;Aicardi-Goutieres syndrome 1;Chilblain lupus 1 (1 variants)
- Aicardi-Goutieres syndrome 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (1 variants)
- Chilblain lupus 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Aicardi-Goutieres syndrome 1;Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (1 variants)
- Systemic lupus erythematosus, susceptibility to (1 variants)
- Chilblain lupus (1 variants)
- Vascular dementia (1 variants)
- Chilblain lupus 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Systemic lupus erythematosus;Aicardi-Goutieres syndrome 1 (1 variants)
- Aicardi-Goutieres syndrome 1;Inborn genetic diseases;Chilblain lupus 1 (1 variants)
- Systemic lupus erythematosus;Chilblain lupus 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Aicardi-Goutieres syndrome 1 (1 variants)
- Aicardi-Goutieres syndrome 1;Systemic lupus erythematosus;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Chilblain lupus 1 (1 variants)
- Vascular dementia;Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (1 variants)
- Retinal dystrophy (1 variants)
- Chilblain lupus 1;Systemic lupus erythematosus;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Aicardi-Goutieres syndrome 1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATRIP 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 | 35 | 42 | ||||
missense | 80 | 90 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region ? | 4 | 3 | 2 | 9 | ||
non coding ? | 24 | 27 | 230 | 87 | 21 | 389 |
Total | 25 | 27 | 316 | 129 | 30 |
Highest pathogenic variant AF is 0.0000328
Variants in ATRIP
This is a list of pathogenic ClinVar variants found in the ATRIP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-48446745-C-G | Benign (Feb 04, 2019) | |||
3-48446788-G-C | Benign (Jul 09, 2018) | |||
3-48446867-G-A | not specified | Uncertain significance (Jan 03, 2024) | ||
3-48446869-C-G | Likely benign (Nov 22, 2023) | |||
3-48446870-A-C | Uncertain significance (Jun 10, 2023) | |||
3-48446871-G-T | Uncertain significance (Dec 17, 2023) | |||
3-48446872-C-G | Uncertain significance (Feb 07, 2023) | |||
3-48446877-G-A | Uncertain significance (Jan 02, 2024) | |||
3-48446877-G-C | Uncertain significance (Oct 20, 2022) | |||
3-48446879-C-T | Uncertain significance (Jan 16, 2024) | |||
3-48446883-G-A | not specified | Uncertain significance (Feb 22, 2023) | ||
3-48446910-C-A | Uncertain significance (Feb 28, 2022) | |||
3-48446925-G-A | Uncertain significance (Jun 08, 2022) | |||
3-48446926-G-C | Likely benign (Apr 11, 2018) | |||
3-48446928-A-AC | Uncertain significance (Jul 17, 2022) | |||
3-48446930-C-G | not specified | Uncertain significance (Jul 11, 2023) | ||
3-48446956-C-T | ATRIP-related disorder | Benign (Jan 28, 2024) | ||
3-48446972-C-A | Uncertain significance (Oct 07, 2022) | |||
3-48447000-A-G | Uncertain significance (Oct 04, 2023) | |||
3-48447019-C-A | Uncertain significance (Feb 09, 2023) | |||
3-48447026-G-A | Uncertain significance (May 18, 2023) | |||
3-48447041-C-T | Uncertain significance (Jan 05, 2024) | |||
3-48447048-C-T | Uncertain significance (Dec 19, 2023) | |||
3-48447062-C-T | Uncertain significance (Jan 25, 2023) | |||
3-48447064-A-G | Likely benign (May 09, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ATRIP | protein_coding | protein_coding | ENST00000320211 | 13 | 19002 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000199 | 1.00 | 125701 | 0 | 47 | 125748 | 0.000187 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.05 | 361 | 422 | 0.856 | 0.0000217 | 5093 |
Missense in Polyphen | 108 | 133.98 | 0.80607 | 1725 | ||
Synonymous | 1.09 | 164 | 183 | 0.897 | 0.0000101 | 1655 |
Loss of Function | 3.22 | 14 | 34.3 | 0.408 | 0.00000173 | 400 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000364 | 0.000364 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000601 | 0.000598 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000203 | 0.000202 |
Middle Eastern | 0.000601 | 0.000598 |
South Asian | 0.000167 | 0.000163 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for checkpoint signaling after DNA damage. Required for ATR expression, possibly by stabilizing the protein. {ECO:0000269|PubMed:12791985}.;
- Pathway
- Fanconi anemia pathway - Homo sapiens (human);miRNA Regulation of DNA Damage Response;DNA Damage Response;HDR through Single Strand Annealing (SSA);HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);Fanconi Anemia Pathway;DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;Generic Transcription Pathway;Homology Directed Repair;RNA Polymerase II Transcription;G2/M DNA damage checkpoint;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Fanconi anemia pathway;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle;Processing of DNA double-strand break ends;ATR signaling pathway;Presynaptic phase of homologous DNA pairing and strand exchange;Homologous DNA Pairing and Strand Exchange;HDR through Homologous Recombination (HRR)
(Consensus)
Recessive Scores
- pRec
- 0.205
Intolerance Scores
- loftool
- 0.793
- rvis_EVS
- -0.75
- rvis_percentile_EVS
- 13.74
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.627
- ghis
- 0.544
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.460
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atrip
- 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- DNA damage checkpoint;DNA replication;interstrand cross-link repair
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- protein binding;K63-linked polyubiquitin modification-dependent protein binding