ATRIP

ATR interacting protein, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 3:48446710-48467645

Links

ENSG00000164053 ∙ NCBI:84126 ∙ OMIM:606605 ∙ HGNC:33499 ∙ Uniprot:Q8WXE1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Seckel syndrome (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATRIP gene.

• Aicardi-Goutieres syndrome 1;Chilblain lupus 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (16 variants)
• Aicardi-Goutieres syndrome 1 (10 variants)
• not provided (7 variants)
• Aicardi-Goutieres syndrome 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Chilblain lupus 1 (4 variants)
• Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Aicardi-Goutieres syndrome 1;Chilblain lupus 1 (3 variants)
• Chilblain lupus 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Aicardi-Goutieres syndrome 1 (3 variants)
• Aicardi-Goutieres syndrome 1, autosomal dominant (2 variants)
• Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Chilblain lupus 1;Aicardi-Goutieres syndrome 1 (2 variants)
• Chilblain lupus 1;Aicardi-Goutieres syndrome 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (2 variants)
• Chilblain lupus (1 variants)
• Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (1 variants)
• Aicardi-Goutieres syndrome 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy;Chilblain lupus 1 (1 variants)
• Seckel syndrome (1 variants)
• Systemic lupus erythematosus (1 variants)
• TREX1-related disorder (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			1	49	6	56
missense			132	7	3	142
nonsense			3			3
start loss						0
frameshift			2			2
inframe indel			3			3
splice donor/acceptor (+/-2bp)	1					1
splice region			5	5	3	13
non coding	36	29	284	139	20	508
Total	37	29	425	195	29

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		not specified	Uncertain significance (May 21, 2024)
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: gnomAD

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: dbNSFP

• 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

• 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