ABLIM1

actin binding LIM protein 1, the group of LIM domain containing

Basic information

Region (hg38): 10:114431110-114768061

Previous symbols: [ "LIMAB1", "ABLIM" ]

Links

ENSG00000099204 ∙ NCBI:3983 ∙ OMIM:602330 ∙ HGNC:78 ∙ Uniprot:O14639 ∙ 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 ABLIM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABLIM1 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						0
missense			51			51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	51	1	0

Variants in ABLIM1

This is a list of pathogenic ClinVar variants found in the ABLIM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-114436328-T-C		not specified	Uncertain significance (May 15, 2024)
10-114436346-C-T		not specified	Uncertain significance (Oct 26, 2022)
10-114436348-C-A		not specified	Uncertain significance (Oct 10, 2023)
10-114437870-T-C		not specified	Uncertain significance (Dec 13, 2023)
10-114437897-T-C		not specified	Uncertain significance (Jan 26, 2022)
10-114439237-C-A		not specified	Uncertain significance (Aug 30, 2021)
10-114441043-T-C		not specified	Uncertain significance (Dec 03, 2021)
10-114441052-T-C		not specified	Uncertain significance (Oct 30, 2023)
10-114441723-C-G		not specified	Uncertain significance (May 17, 2023)
10-114441723-C-T		not specified	Uncertain significance (Aug 23, 2021)
10-114444068-A-G		not specified	Uncertain significance (Oct 05, 2023)
10-114444079-C-T		not specified	Uncertain significance (Apr 07, 2023)
10-114444080-G-A		not specified	Uncertain significance (Nov 16, 2021)
10-114445368-C-T		not specified	Uncertain significance (May 09, 2024)
10-114445397-T-C		not specified	Uncertain significance (Mar 22, 2023)
10-114447925-T-A		not specified	Uncertain significance (Dec 20, 2023)
10-114447934-T-A		not specified	Uncertain significance (Feb 12, 2024)
10-114447994-A-C		not specified	Uncertain significance (Sep 20, 2023)
10-114453409-C-T		not specified	Uncertain significance (Sep 16, 2021)
10-114453442-G-A		not specified	Uncertain significance (May 13, 2024)
10-114453451-G-C		not specified	Uncertain significance (Mar 30, 2024)
10-114453454-G-T		not specified	Uncertain significance (Jul 09, 2021)
10-114453466-C-T		not specified	Uncertain significance (Jan 31, 2022)
10-114465724-C-T		not specified	Uncertain significance (Sep 28, 2021)
10-114465730-G-A		not specified	Uncertain significance (Sep 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABLIM1	protein_coding	protein_coding	ENST00000277895	23	253891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.930	0.0699	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.62	376	475	0.791	0.0000284	5091
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000549	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;DCC mediated attractive signaling;Netrin-1 signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.207
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.28

Haploinsufficiency Scores

• pHI: 0.247
• hipred: Y
• hipred_score: 0.639
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ablim1
• Phenotype: normal phenotype

Gene ontology

• Biological process: cytoskeleton organization;visual perception;animal organ morphogenesis;lamellipodium assembly;cilium assembly
• Cellular component: stress fiber;cytoplasm;actin cytoskeleton;lamellipodium
• Molecular function: actin binding;protein binding;metal ion binding;actin filament binding