ABR

ABR activator of RhoGEF and GTPase, the group of Dbl family Rho GEFs|Pleckstrin homology domain containing|MicroRNA protein coding host genes|C2 domain containing

Basic information

Region (hg38): 17:1003518-1229738

Links

ENSG00000159842 ∙ NCBI:29 ∙ OMIM:600365 ∙ HGNC:81 ∙ Uniprot:Q12979 ∙ 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 ABR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABR 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	1	2
missense			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	33	3	1

Variants in ABR

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

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

Position	Type	Phenotype	Significance	ClinVar
17-1006124-C-T		not specified	Uncertain significance (Jul 20, 2021)
17-1006129-G-A		not specified	Uncertain significance (Oct 27, 2023)
17-1006153-T-A		not specified	Uncertain significance (Aug 01, 2022)
17-1007161-G-A			Benign (Dec 31, 2019)
17-1007169-G-A		not specified	Uncertain significance (May 25, 2022)
17-1007305-C-T		not specified	Uncertain significance (Oct 25, 2023)
17-1009690-T-A		not specified	Uncertain significance (Oct 06, 2021)
17-1009736-C-T		not specified	Uncertain significance (Apr 29, 2024)
17-1010732-T-C		not specified	Uncertain significance (Jan 04, 2022)
17-1010758-C-T		not specified	Uncertain significance (May 18, 2022)
17-1010790-G-C			Uncertain significance (Jul 05, 2023)
17-1010813-C-T		not specified	Uncertain significance (Aug 17, 2021)
17-1010843-T-C		not specified	Uncertain significance (May 23, 2023)
17-1011852-C-T		not specified	Uncertain significance (Jan 04, 2024)
17-1011868-C-T			Likely benign (Mar 01, 2022)
17-1011880-C-T		not specified	Likely benign (Apr 09, 2024)
17-1011885-C-T		not specified	Uncertain significance (Feb 14, 2023)
17-1011888-C-T		not specified	Uncertain significance (May 18, 2022)
17-1011957-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-1012691-G-A		not specified	Uncertain significance (Dec 17, 2023)
17-1013122-C-T		not specified	Uncertain significance (Feb 16, 2023)
17-1050082-C-T		not specified	Uncertain significance (Jan 04, 2022)
17-1050132-T-C		not specified	Uncertain significance (Feb 05, 2024)
17-1050602-C-T		not specified	Uncertain significance (Jun 29, 2022)
17-1056089-A-G		ABR-related disorder	Likely benign (May 21, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABR	protein_coding	protein_coding	ENST00000302538	23	225558

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.627	0.373	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.89	269	518	0.519	0.0000315	5631
Missense in Polyphen		84	187.35	0.44836		1947
Synonymous	-0.521	239	229	1.04	0.0000158	1631
Loss of Function	5.00	10	47.0	0.213	0.00000226	559

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000913	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for RAC and CDC42. Promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them.
• Pathway: Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Regulation of RAC1 activity;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity (Consensus)

Intolerance Scores

• loftool: 0.319
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.8

Haploinsufficiency Scores

• pHI: 0.593
• hipred: Y
• hipred_score: 0.774
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.528

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abr
• Phenotype: cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear 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); normal phenotype

Gene ontology

• Biological process: negative regulation of cellular extravasation;G protein-coupled receptor signaling pathway;small GTPase mediated signal transduction;brain development;actin cytoskeleton organization;response to lipopolysaccharide;regulation of Rho protein signal transduction;inner ear morphogenesis;positive regulation of apoptotic process;regulation of vascular permeability;negative regulation of neutrophil degranulation;positive regulation of GTPase activity;negative regulation of inflammatory response;positive regulation of phagocytosis;modulation of chemical synaptic transmission;neuromuscular process controlling balance;regulation of small GTPase mediated signal transduction;negative regulation of blood vessel remodeling
• Cellular component: cytosol;plasma membrane;membrane;Schaffer collateral - CA1 synapse;glutamatergic synapse
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity