ABLIM3

actin binding LIM protein family member 3, the group of LIM domain containing

Basic information

Region (hg38): 5:149141482-149260542

Links

ENSG00000173210 ∙ NCBI:22885 ∙ OMIM:611305 ∙ HGNC:29132 ∙ Uniprot:O94929 ∙ 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 ABLIM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABLIM3 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					3	3
missense			48			48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	49	0	3

Variants in ABLIM3

This is a list of pathogenic ClinVar variants found in the ABLIM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-149183481-C-T		not specified	Uncertain significance (Mar 30, 2024)
5-149183496-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-149198309-G-A		not specified	Uncertain significance (Sep 14, 2022)
5-149198318-G-A		not specified	Uncertain significance (Dec 07, 2023)
5-149198323-C-T		not specified	Uncertain significance (Jul 20, 2021)
5-149198324-G-A		not specified	Uncertain significance (Aug 26, 2022)
5-149198327-A-C		not specified	Uncertain significance (Apr 08, 2024)
5-149198363-G-A		not specified	Uncertain significance (Mar 21, 2024)
5-149198386-G-A		not specified	Uncertain significance (Feb 01, 2023)
5-149200330-T-C		not specified	Uncertain significance (Apr 08, 2022)
5-149200412-G-A			Benign (May 04, 2018)
5-149207016-G-A		not specified	Uncertain significance (Oct 14, 2021)
5-149207022-A-G		not specified	Uncertain significance (Jan 22, 2024)
5-149217001-C-T		not specified	Uncertain significance (Dec 21, 2022)
5-149230654-G-A		not specified	Uncertain significance (Dec 22, 2023)
5-149230673-G-A		not specified	Uncertain significance (Mar 17, 2023)
5-149230687-C-T		not specified	Uncertain significance (Oct 06, 2022)
5-149230688-G-A		not specified	Uncertain significance (Jul 06, 2021)
5-149233250-T-C		not specified	Uncertain significance (Jan 10, 2022)
5-149233299-G-A		not specified	Uncertain significance (Jun 21, 2023)
5-149237449-C-T		not specified	Uncertain significance (Nov 27, 2023)
5-149237517-G-A		not specified	Uncertain significance (May 09, 2022)
5-149237527-G-A		not specified	Uncertain significance (Dec 07, 2023)
5-149237554-A-T		not specified	Uncertain significance (Feb 02, 2023)
5-149239258-C-T		not specified	Uncertain significance (Nov 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABLIM3	protein_coding	protein_coding	ENST00000506113	23	119060

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-7	1.00	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.696	381	421	0.905	0.0000258	4461
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000111	0.000109
South Asian	0.000163	0.000163
Other	0.00	0.00

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: 0.108

Intolerance Scores

• loftool: 0.379
• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.29

Haploinsufficiency Scores

• pHI: 0.447
• hipred: Y
• hipred_score: 0.540
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ablim3

Gene ontology

• Biological process: transcription, DNA-templated;lamellipodium assembly;actin cytoskeleton organization;positive regulation of transcription by RNA polymerase II;cilium assembly;positive regulation of protein targeting to mitochondrion
• Cellular component: stress fiber;cytoplasm;actin cytoskeleton;lamellipodium;glutamatergic synapse
• Molecular function: protein binding;metal ion binding;actin filament binding