GeneBe

ABCA2

ATP binding cassette subfamily A member 2, the group of ATP binding cassette subfamily A

Basic information

Region (hg38): 9:137007234-137028915

Previous symbols: [ "ABC2" ]

Links

ENSG00000107331 ∙ NCBI:20 ∙ OMIM:600047 ∙ HGNC:32 ∙ Uniprot:Q9BZC7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • schizophrenia (Limited), mode of inheritance: Unknown
  • intellectual developmental disorder with poor growth and with or without seizures or ataxia (Moderate), mode of inheritance: AR
  • intellectual developmental disorder with poor growth and with or without seizures or ataxia (Strong), mode of inheritance: AR
  • intellectual developmental disorder with poor growth and with or without seizures or ataxia (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder with poor growth and with or without seizures or ataxiaARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic29302074; 30237576; 31047799

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCA2 gene.

  • not_specified (335 variants)
  • not_provided (172 variants)
  • ABCA2-related_disorder (50 variants)
  • Intellectual_developmental_disorder_with_poor_growth_and_with_or_without_seizures_or_ataxia (44 variants)
  • Ataxia_with_Dysarthria (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCA2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001606.5. 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.

EffectPLPVUSLBBSum
synonymous
11
clinvar
89
clinvar
10
clinvar
 110
missense
1
clinvar
406
clinvar
19
clinvar
2
clinvar
 428
nonsense
2
clinvar
2
clinvar
2
clinvar
 6
start loss
0
frameshift
6
clinvar
2
clinvar
 8
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
11
clinvar
 14
Total 10 6 430 108 12

Highest pathogenic variant AF is 6.855692e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ABCA2protein_codingprotein_codingENST00000341511 4921682
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.001.30e-101244400321244720.000129
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense4.9110291.58e+30.6520.00011315623
Missense in Polyphen314693.660.452676845
Synonymous-3.368497331.160.00005935063
Loss of Function8.92121150.1040.000005491254

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001980.000193
Ashkenazi Jewish0.0002030.000199
East Asian0.0001670.000167
Finnish0.0001150.0000928
European (Non-Finnish)0.0001690.000151
Middle Eastern0.0001670.000167
South Asian0.0001710.000163
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probable transporter, its natural substrate has not been found yet. May have a role in macrophage lipid metabolism and neural development.;
Pathway
Lysosome - Homo sapiens (human);ABC transporters - Homo sapiens (human);ABC transporters in lipid homeostasis;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

pRec
0.298

Intolerance Scores

loftool
0.00985
rvis_EVS
-4.24
rvis_percentile_EVS
0.12

Haploinsufficiency Scores

pHI
0.346
hipred
Y
hipred_score
0.639
ghis
0.636

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.888

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Abca2
Phenotype
growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); reproductive system phenotype; 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);

Gene ontology

Biological process
regulation of transcription by RNA polymerase II;lipid metabolic process;lipid transport;regulation of intracellular cholesterol transport;response to drug;cholesterol homeostasis;response to steroid hormone;transmembrane transport;response to cholesterol
Cellular component
lysosome;lysosomal membrane;endosome;microtubule organizing center;endosome membrane;membrane;integral component of membrane;cytoplasmic vesicle;ATP-binding cassette (ABC) transporter complex;intracellular membrane-bounded organelle
Molecular function
nucleotide binding;lipid transporter activity;ATP binding;ATPase activity;ATPase activity, coupled to transmembrane movement of substances