IGLL5

immunoglobulin lambda like polypeptide 5, the group of C1-set domain containing

Basic information

Region (hg38): 22:22887780-22896111

Links

ENSG00000254709 ∙ NCBI:100423062 ∙ ∙ HGNC:38476 ∙ Uniprot:B9A064 ∙ 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 IGLL5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGLL5 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			21	4		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	4	0

Variants in IGLL5

This is a list of pathogenic ClinVar variants found in the IGLL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-22888063-A-C		not specified	Uncertain significance (Dec 16, 2022)
22-22888136-T-G		not specified	Uncertain significance (Jan 04, 2024)
22-22888157-C-T		not specified	Uncertain significance (Mar 14, 2023)
22-22888171-C-T		not specified	Uncertain significance (Jul 09, 2024)
22-22888172-G-A		not specified	Uncertain significance (Oct 22, 2021)
22-22888174-C-T		not specified	Uncertain significance (May 23, 2023)
22-22888205-A-G		not specified	Likely benign (Oct 04, 2024)
22-22888232-G-C		not specified	Uncertain significance (Feb 15, 2023)
22-22888234-T-A		not specified	Uncertain significance (Nov 12, 2024)
22-22893729-C-T		not specified	Uncertain significance (Jan 09, 2024)
22-22893816-T-C		not specified	Uncertain significance (May 04, 2023)
22-22895393-C-T		not specified	Uncertain significance (Dec 15, 2023)
22-22895476-C-T		not specified	Uncertain significance (Jan 16, 2024)
22-22895489-C-A		not specified	Likely benign (May 23, 2024)
22-22895494-G-A		not specified	Uncertain significance (Mar 24, 2023)
22-22895518-G-A		not specified	Likely benign (Nov 29, 2023)
22-22895543-A-C		not specified	Likely benign (Sep 14, 2021)
22-22895557-A-C		not specified	Uncertain significance (Dec 15, 2023)
22-22895573-C-T		not specified	Uncertain significance (Jun 11, 2021)
22-22895585-A-G		not specified	Uncertain significance (Aug 15, 2024)
22-22895597-C-T		not specified	Uncertain significance (Mar 07, 2025)
22-22895634-C-G		not specified	Uncertain significance (Oct 25, 2024)
22-22895636-A-G		not specified	Uncertain significance (Nov 21, 2022)
22-22895642-C-T		not specified	Uncertain significance (Feb 08, 2025)
22-22895659-G-A		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGLL5	protein_coding	protein_coding	ENST00000526893	3	8328

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.19e-10	0.00900	122874	0	4	122878	0.0000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-6.44	310	115	2.69	0.00000692	1261
Missense in Polyphen		30	22.377	1.3407		318
Synonymous	-8.40	128	51.4	2.49	0.00000340	429
Loss of Function	-2.18	11	5.48	2.01	3.21e-7	47

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000695	0.0000655
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000272
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

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;complement activation, classical pathway;defense response to bacterium;innate immune response;B cell receptor signaling pathway;positive regulation of B cell activation
• Cellular component: external side of plasma membrane;immunoglobulin complex, circulating;extracellular exosome
• Molecular function: antigen binding;immunoglobulin receptor binding