ISL2

ISL LIM homeobox 2, the group of LIM class homeoboxes

Basic information

Region (hg38): 15:76336773-76342475

Links

ENSG00000159556 ∙ NCBI:64843 ∙ OMIM:609481 ∙ HGNC:18524 ∙ Uniprot:Q96A47 ∙ 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 ISL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISL2 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in ISL2

This is a list of pathogenic ClinVar variants found in the ISL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-76336909-C-G		not specified	Uncertain significance (Mar 07, 2025)
15-76336931-T-G		not specified	Uncertain significance (Oct 17, 2024)
15-76337796-T-C		not specified	Uncertain significance (May 10, 2023)
15-76338310-A-T		not specified	Uncertain significance (Sep 17, 2021)
15-76338340-G-C		not specified	Uncertain significance (Sep 24, 2024)
15-76338358-G-T		not specified	Uncertain significance (Oct 07, 2024)
15-76338390-G-C		not specified	Uncertain significance (Nov 18, 2023)
15-76338403-G-C		not specified	Uncertain significance (Oct 21, 2024)
15-76338404-A-T		not specified	Uncertain significance (Jan 26, 2023)
15-76338439-C-G		not specified	Uncertain significance (Jul 25, 2024)
15-76338445-G-C		not specified	Uncertain significance (Aug 08, 2022)
15-76338448-C-T		not specified	Uncertain significance (Feb 10, 2025)
15-76338499-G-C		not specified	Uncertain significance (Oct 24, 2023)
15-76340285-C-T		not specified	Uncertain significance (Oct 06, 2024)
15-76340287-G-A		not specified	Uncertain significance (Apr 12, 2022)
15-76340290-C-G		not specified	Uncertain significance (May 03, 2023)
15-76340327-C-G		not specified	Uncertain significance (May 03, 2023)
15-76340402-A-G		not specified	Uncertain significance (Mar 01, 2025)
15-76340459-C-T		not specified	Uncertain significance (Jan 02, 2024)
15-76340516-T-C		not specified	Uncertain significance (Jul 23, 2024)
15-76341168-C-T		not specified	Uncertain significance (Jun 30, 2023)
15-76341261-C-T		not specified	Uncertain significance (Sep 22, 2023)
15-76341288-C-T		not specified	Uncertain significance (Feb 13, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISL2	protein_coding	protein_coding	ENST00000290759	6	5753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.111	0.883	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	150	199	0.755	0.00000891	2317
Missense in Polyphen		34	70.048	0.48538		766
Synonymous	-1.20	102	87.7	1.16	0.00000414	710
Loss of Function	2.42	4	13.7	0.293	5.83e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000913	0.0000908
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional factor that defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways. {ECO:0000250}.

Recessive Scores

• pRec: 0.155

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.598
• hipred: Y
• hipred_score: 0.623
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Isl2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: isl2a
• Affected structure: angioblastic mesenchymal cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;spinal cord motor neuron cell fate specification;visceral motor neuron differentiation;retinal ganglion cell axon guidance;negative regulation of neuron differentiation;neuron development;peripheral nervous system neuron development
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;sequence-specific DNA binding;metal ion binding