ILDR2

immunoglobulin like domain containing receptor 2

Basic information

Region (hg38): 1:166895711-166975540

Previous symbols: [ "C1orf32" ]

Links

ENSG00000143195 ∙ NCBI:387597 ∙ OMIM:618081 ∙ HGNC:18131 ∙ Uniprot:Q71H61 ∙ 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 ILDR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ILDR2 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					1	1
missense			50	1		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	1	1

Variants in ILDR2

This is a list of pathogenic ClinVar variants found in the ILDR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-166920714-T-A		not specified	Uncertain significance (Feb 09, 2025)
1-166920717-G-A		not specified	Uncertain significance (Mar 03, 2025)
1-166920741-T-C		not specified	Uncertain significance (Jan 16, 2024)
1-166920759-G-A		not specified	Uncertain significance (Sep 27, 2022)
1-166920793-T-C		not specified	Uncertain significance (Dec 06, 2022)
1-166920826-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-166920847-C-A		not specified	Uncertain significance (Aug 22, 2022)
1-166920870-T-C		not specified	Uncertain significance (Sep 22, 2023)
1-166920912-G-A		not specified	Uncertain significance (Jun 12, 2023)
1-166920924-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-166920931-G-A		not specified	Uncertain significance (Jul 28, 2021)
1-166920939-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-166920958-C-G		not specified	Uncertain significance (Jan 27, 2025)
1-166920997-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-166921014-T-G		not specified	Uncertain significance (Nov 02, 2023)
1-166921046-G-T		not specified	Uncertain significance (Dec 21, 2022)
1-166921059-G-A		not specified	Uncertain significance (Jun 26, 2024)
1-166921084-T-C		not specified	Uncertain significance (May 04, 2023)
1-166921126-T-C		not specified	Uncertain significance (Feb 15, 2023)
1-166921143-C-A		not specified	Uncertain significance (Oct 11, 2024)
1-166921149-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-166921159-A-C		not specified	Uncertain significance (Nov 09, 2024)
1-166921173-G-T		not specified	Uncertain significance (Sep 27, 2022)
1-166921198-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-166921224-C-T		not specified	Uncertain significance (Feb 05, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ILDR2	protein_coding	protein_coding	ENST00000271417	10	62277

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0462	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	273	338	0.808	0.0000179	4092
Missense in Polyphen		93	132.52	0.70179		1607
Synonymous	0.460	129	136	0.950	0.00000744	1262
Loss of Function	4.13	4	27.3	0.147	0.00000130	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000811	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000203	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in lipid homeostasis and ER stress pathways. {ECO:0000250}.

Recessive Scores

• pRec: 0.0914

Intolerance Scores

• loftool: 0.524
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.397
• hipred: Y
• hipred_score: 0.630
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ildr2
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: ildr2
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: response to glucose;insulin secretion;cell differentiation;pancreas development;homeostasis of number of cells within a tissue
• Cellular component: endoplasmic reticulum membrane;integral component of membrane