GeneBe

ABCA6

ATP binding cassette subfamily A member 6, the group of ATP binding cassette subfamily A|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:69078702-69141895

Links

ENSG00000154262 ∙ NCBI:23460 ∙ OMIM:612504 ∙ HGNC:36 ∙ Uniprot:Q8N139 ∙ 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 ABCA6 gene.

  • not_specified (201 variants)
  • not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCA6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000080284.3. 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.

EffectPLPVUSLBBSum
synonymous
6
clinvar
 6
missense
186
clinvar
14
clinvar
 200
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 186 20 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ABCA6protein_codingprotein_codingENST00000284425 3863187
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
5.11e-270.79312527924671257480.00187
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4918247851.050.000037710601
Missense in Polyphen221219.021.00913288
Synonymous0.5842672790.9560.00001412947
Loss of Function2.555478.40.6890.000003571116

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.01370.0131
Ashkenazi Jewish0.005790.00577
East Asian0.001670.00152
Finnish0.0002850.000277
European (Non-Finnish)0.0009610.000932
Middle Eastern0.001670.00152
South Asian0.001240.00105
Other0.001640.00147

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probable transporter which may play a role in macrophage lipid homeostasis.;
Pathway
ABC transporters - Homo sapiens (human);ABC transporters in lipid homeostasis;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

pRec
0.105

Intolerance Scores

loftool
0.0858
rvis_EVS
0.26
rvis_percentile_EVS
70.44

Haploinsufficiency Scores

pHI
0.0466
hipred
N
hipred_score
0.214
ghis
0.482

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.116

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Abca6
Phenotype
hematopoietic 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); homeostasis/metabolism phenotype;

Gene ontology

Biological process
lipid transport;transmembrane transport
Cellular component
nucleoplasm;integral component of membrane;intracellular membrane-bounded organelle
Molecular function
lipid transporter activity;ATP binding;ATPase activity, coupled to transmembrane movement of substances