ABLIM2

protein-coding

actin binding LIM protein family member 2, the group of LIM domain containing|MicroRNA protein coding host genes

Gene summary

Predicted to enable actin filament binding activity. Predicted to be involved in lamellipodium assembly. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Located in actin cytoskeleton. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001130083.2

Inheritance

—

ClinVar variants

U:136B:7

Top phenotype

High myopia

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr4:7,965,310-8,158,832

External References & Databases

Ensembl (ENSG00000163995)

Transcript & Mutation Effects

hg38 • Region Span ~193.5 kb

Loading mutation effect viewer...

GenCC 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 ABLIM2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 125

not providedTotal: 4

High myopiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001130083.2. 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			2 clinvar	3 clinvar		5
missense			125 clinvar	4 clinvar		129
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	136	7	0	143

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 71 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001130083.2	RefSeq	NP_001123555.1	21	MANE Select
ENST00000447017.7	Ensembl	ENSP00000393511.2	21	MANE Select
NM_001130084.2	RefSeq	NP_001123556.1	20	Standard
NM_001130085.2	RefSeq	NP_001123557.1	18	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

Molecular Function

metal ion binding
actin filament binding

Cellular Component

cytoplasm
actin cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000447017
Coding exons: 21
Length: 193521
Individuals with no LoFs: 124666
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 124700
p: 0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.166	391	400	0.977	0.0000255	4199
Missense (PolyPhen)		136	141.35	0.96218		1368
Synonymous	-1.35	191	169	1.13	0.0000120	1188
Loss of Function	4.37	13	44.5	0.292	0.00000264	468

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00052	0.00050	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00017	0.00016	rare
South Asian	0.00011	0.000098	rare
Other	0.00050	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity. {ECO:0000269|PubMed:17194709}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.295
RVIS EVS: -1.51
RVIS percentile EVS: 3.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.922

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium