ABLIM1
protein-codingactin binding LIM protein 1, the group of LIM domain containing
Gene summary
This gene encodes a LIM zinc-binding domain-containing protein that binds to actin filaments and mediates interactions between actin and cytoplasmic targets. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2017]
- LIMAB1
- ABLIM
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~337.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ABLIM1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002313.7. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 120 | 1 | 121 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 1 | 8 | |||
| Total | 0 | 0 | 127 | 2 | 0 | 129 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002304.3 | 23 | MANE Select | |
| Ensembl | ENSP00000433629.3 | 23 | MANE Select | |
| RefSeq | NP_001003407.1 | 23 | Standard | |
| RefSeq | NP_001309811.1 | 24 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Axon guidance - Homo sapiens (human)
- Developmental Biology
- DCC mediated attractive signaling
- Netrin-1 signaling
- Axon guidance
Biological Process
- cytoskeleton organization
- visual perception
- animal organ morphogenesis
- lamellipodium assembly
- cilium assembly
Molecular Function
- actin binding
- protein binding
- metal ion binding
- actin filament binding
Cellular Component
- stress fiber
- cytoplasm
- actin cytoskeleton
- lamellipodium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000277895
- Coding exons
- 23
- Length
- 253891
- Individuals with no LoFs
- 125732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 125747
- p
- 0.0000596
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.62 | 376 | 475 | 0.791 | 0.0000284 | 5091 |
| Missense (PolyPhen) | 91 | 148.26 | 0.61378 | 1609 | ||
| Synonymous | 0.0790 | 171 | 172 | 0.992 | 0.0000105 | 1448 |
| Loss of Function | 5.23 | 9 | 48.2 | 0.187 | 0.00000248 | 568 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000055 | 0.000053 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May act as scaffold protein (By similarity). May play a role in the development of the retina. Has been suggested to play a role in axon guidance. {ECO:0000250, ECO:0000269|PubMed:9245787}.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- LoFtool
- 0.207
- RVIS EVS
- -0.24
- RVIS percentile EVS
- 36.28
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.799
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |