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): 17:1003519-1229738

Links

ENSG00000159842 ∙ NCBI:29 ∙ OMIM:600365 ∙ HGNC:81 ∙ Uniprot:Q12979 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 28.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_021962.5	NP_068781.2	23	yes	-
ENST00000302538.10	ENSP00000303909.5	23	yes	-
NM_001092.5	NP_001083.2	22	-	-
NM_001159746.3	NP_001153218.1	22	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not_specified (91 variants)
• not_provided (3 variants)
• ABR-related_disorder (2 variants)

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. These statistics are base on transcript: NM_021962.5. 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			1	2	1	4
missense			92	2		94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	96	4	1

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
		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

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

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