IGLL1

immunoglobulin lambda like polypeptide 1, the group of CD molecules|C1-set domain containing

Basic information

Region (hg38): 22:23573124-23580302

Previous symbols: [ "IGLL" ]

Links

ENSG00000128322 ∙ NCBI:3543 ∙ OMIM:146770 ∙ HGNC:5870 ∙ Uniprot:P15814 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• agammaglobulinemia 2, autosomal recessive (Limited), mode of inheritance: AR
• autosomal agammaglobulinemia (Supportive), mode of inheritance: AD
• agammaglobulinemia 2, autosomal recessive (Limited), mode of inheritance: Unknown
• agammaglobulinemia 2, autosomal recessive (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Agammaglobulinemia 2, autosomal recessive	AR	Allergy/Immunology/Infectious	Antiinfectious prophylaxis (including with administration of IVIG) and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	9419212; 10077633; 10590911

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IGLL1 gene.

• Agammaglobulinemia 2, autosomal recessive (177 variants)
• not provided (21 variants)
• Inborn genetic diseases (13 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGLL1 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	39	8	49
missense			79	12	12	103
nonsense			1			1
start loss						0
frameshift			9			9
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			7	3		10
non coding				3	8	11
Total	0	0	92	54	28

Variants in IGLL1

This is a list of pathogenic ClinVar variants found in the IGLL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-23573153-T-G			Benign (Jun 19, 2021)
22-23573183-G-A			Benign (Jun 19, 2021)
22-23573270-G-A		not specified	Uncertain significance (Jan 31, 2024)
22-23573275-T-C		Agammaglobulinemia 2, autosomal recessive	Likely benign (Mar 17, 2023)
22-23573284-G-A		Agammaglobulinemia 2, autosomal recessive	Benign (Mar 16, 2023)
22-23573289-C-T		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Nov 01, 2022)
22-23573290-C-T		Agammaglobulinemia 2, autosomal recessive	Likely benign (Dec 20, 2023)
22-23573291-G-A		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Oct 05, 2023)
22-23573292-T-A		Agammaglobulinemia 2, autosomal recessive	Conflicting classifications of pathogenicity (Dec 20, 2023)
22-23573294-T-A		not specified	Uncertain significance (Aug 16, 2022)
22-23573299-C-T		Agammaglobulinemia 2, autosomal recessive	Likely benign (Dec 18, 2023)
22-23573299-CACG-TGCA		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Apr 23, 2019)
22-23573300-A-G		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Dec 18, 2023)
22-23573300-ACG-A		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Aug 28, 2021)
22-23573301-C-T		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Nov 25, 2023)
22-23573302-G-A		Agammaglobulinemia 2, autosomal recessive	Likely benign (Dec 18, 2023)
22-23573302-G-C		Agammaglobulinemia 2, autosomal recessive	Likely benign (Aug 20, 2022)
22-23573303-G-C		Agammaglobulinemia 2, autosomal recessive • not specified	Uncertain significance (Nov 10, 2023)
22-23573313-C-T		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Dec 08, 2022)
22-23573314-G-A		Agammaglobulinemia 2, autosomal recessive	Likely benign (Feb 01, 2024)
22-23573314-G-T		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Jan 11, 2024)
22-23573318-A-C		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Jun 24, 2021)
22-23573318-A-G		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Oct 13, 2023)
22-23573320-G-A		Agammaglobulinemia 2, autosomal recessive	Likely benign (Jan 11, 2024)
22-23573323-C-A		Agammaglobulinemia 2, autosomal recessive	Uncertain significance (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGLL1	protein_coding	protein_coding	ENST00000330377	3	7184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0139	0.690	125492	1	247	125740	0.000987

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.298	134	125	1.07	0.00000793	1326
Missense in Polyphen		23	21.311	1.0793		281
Synonymous	-1.52	73	58.2	1.25	0.00000419	452
Loss of Function	0.596	3	4.34	0.691	1.87e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000593	0.000593
Ashkenazi Jewish	0.00179	0.00179
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00178	0.00178
Middle Eastern	0.00	0.00
South Asian	0.000294	0.000261
Other	0.000651	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Critical for B-cell development. {ECO:0000269|PubMed:9419212}.
• Pathway: Primary immunodeficiency - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.285

Haploinsufficiency Scores

• pHI: 0.0666
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igll1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: phagocytosis, recognition;phagocytosis, engulfment;immune response;complement activation, classical pathway;defense response to bacterium;innate immune response;B cell receptor signaling pathway;positive regulation of B cell activation;leukocyte migration
• Cellular component: extracellular region;external side of plasma membrane;membrane;immunoglobulin complex, circulating
• Molecular function: antigen binding;immunoglobulin receptor binding