ABLIM2

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

Basic information

Region (hg38): 4:7965309-8158832

Links

ENSG00000163995 ∙ NCBI:84448 ∙ OMIM:612544 ∙ HGNC:19195 ∙ Uniprot:Q6H8Q1 ∙ 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 ABLIM2 gene.

• Inborn genetic diseases (35 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABLIM2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			34	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	34	4	0

Variants in ABLIM2

This is a list of pathogenic ClinVar variants found in the ABLIM2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-7967015-A-G		not specified	Uncertain significance (Jun 01, 2023)
4-7983284-C-T		not specified	Uncertain significance (Aug 15, 2023)
4-7983301-A-G		not specified	Uncertain significance (Jun 17, 2022)
4-7983304-C-T		High myopia	Uncertain significance (Dec 17, 2018)
4-7983320-C-T		not specified	Uncertain significance (Mar 16, 2022)
4-7984864-G-T		not specified	Uncertain significance (May 23, 2023)
4-7984871-C-T		not specified	Uncertain significance (Nov 14, 2023)
4-7984880-G-T		not specified	Uncertain significance (Mar 07, 2024)
4-7984886-T-C		not specified	Uncertain significance (Oct 12, 2022)
4-7992867-C-T		not specified	Uncertain significance (Aug 01, 2022)
4-8008096-G-T		not specified	Uncertain significance (Dec 19, 2023)
4-8008161-T-C		not specified	Uncertain significance (Mar 22, 2023)
4-8009080-C-A		not specified	Uncertain significance (Sep 06, 2022)
4-8009100-C-A		not specified	Uncertain significance (Nov 15, 2021)
4-8020205-G-C		not specified	Uncertain significance (Aug 02, 2021)
4-8020208-C-A		not specified	Uncertain significance (Oct 04, 2022)
4-8020208-C-T		not specified	Uncertain significance (Jul 20, 2022)
4-8020230-C-G		not specified	Uncertain significance (Oct 10, 2023)
4-8020249-G-A		not specified	Uncertain significance (Jun 13, 2023)
4-8020268-C-T		not specified	Uncertain significance (Jan 02, 2024)
4-8020300-C-T		not specified	Uncertain significance (Jun 10, 2022)
4-8027845-C-T		not specified	Uncertain significance (Jun 23, 2023)
4-8029700-C-T		not specified	Uncertain significance (Jun 13, 2023)
4-8029760-C-T		not specified	Uncertain significance (Aug 08, 2023)
4-8036169-C-A		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABLIM2	protein_coding	protein_coding	ENST00000447017	21	193521

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00459	0.995	124666	0	34	124700	0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.166	391	400	0.977	0.0000255	4199
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000524	0.000497
East Asian	0.000114	0.000111
Finnish	0.0000933	0.0000928
European (Non-Finnish)	0.000165	0.000159
Middle Eastern	0.000114	0.000111
South Asian	0.000106	0.0000980
Other	0.000497	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity. {ECO:0000269|PubMed:17194709}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;DCC mediated attractive signaling;Netrin-1 signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.295
• rvis_EVS: -1.51
• rvis_percentile_EVS: 3.54

Haploinsufficiency Scores

• pHI: 0.236
• hipred: Y
• hipred_score: 0.604
• ghis: 0.655

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ablim2

Gene ontology

• Biological process: transcription, DNA-templated;lamellipodium assembly;actin cytoskeleton organization
• Cellular component: cytoplasm;actin cytoskeleton
• Molecular function: metal ion binding;actin filament binding