ABLIM3
protein-codingactin binding LIM protein family member 3, the group of LIM domain containing
Gene summary
This gene encodes a member of the actin-binding LIM (abLIM) family of proteins. These proteins are characterized by an N-terminal LIM domain and a C-terminal dematin-like domain. The encoded protein interacts with actin filaments and may be a component of adherens junctions in several cell types. A variant of this gene may be associated with pain sensitivity in male human patients. [provided by RefSeq, Sep 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~119.1 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 ABLIM3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014945.5. 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 | 3 | 3 | 6 | |||
| missense | 121 | 121 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 125 | 0 | 3 | 128 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055760.1 | 23 | MANE Select | |
| Ensembl | ENSP00000310309.7 | 23 | MANE Select | |
| RefSeq | NP_001287944.1 | 23 | Standard | |
| RefSeq | NP_001287947.1 | 22 | 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
- transcription, DNA-templated
- lamellipodium assembly
- actin cytoskeleton organization
- positive regulation of transcription by RNA polymerase II
- cilium assembly
Molecular Function
- protein binding
- metal ion binding
- actin filament binding
Cellular Component
- stress fiber
- cytoplasm
- actin cytoskeleton
- lamellipodium
- glutamatergic synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000506113
- Coding exons
- 23
- Length
- 119060
- Individuals with no LoFs
- 125710
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 38
- Defined
- 125748
- p
- 0.000151
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.696 | 381 | 421 | 0.905 | 0.0000258 | 4461 |
| Missense (PolyPhen) | 123 | 157.11 | 0.78288 | 1593 | ||
| Synonymous | 1.09 | 139 | 156 | 0.889 | 0.00000925 | 1264 |
| Loss of Function | 3.91 | 21 | 51.2 | 0.410 | 0.00000288 | 551 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity. {ECO:0000269|PubMed:17194709}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.379
- RVIS EVS
- -1.15
- RVIS percentile EVS
- 6.29
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.912
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |