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
• breast cancer (Moderate), mode of inheritance: AD

ClinVar

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

• not_specified (883 variants)
• not_provided (259 variants)
• ATRIP-related_disorder (7 variants)
• Microcephalic_Primordial_Dwarfism_with_immunodeficiency (2 variants)
• Seckel_syndrome (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. These statistics are base on transcript: NM_000130384.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			7	259	2	268
missense			578	52	2	632
nonsense			9			9
start loss						0
frameshift			13			13
splice donor/acceptor (+/-2bp)		1	4			5
Total	0	1	611	311	4

Highest pathogenic variant AF is 0.00000325759

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