LGALS9B

galectin 9B, the group of Galectins

Basic information

Region (hg38): 17:20449395-20467539

Links

ENSG00000170298 ∙ NCBI:284194 ∙ ∙ HGNC:24842 ∙ Uniprot:Q3B8N2 ∙ 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 LGALS9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS9B 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			24	3	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	4	1

Variants in LGALS9B

This is a list of pathogenic ClinVar variants found in the LGALS9B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-20449985-G-A			Likely benign (Jan 01, 2023)
17-20450046-C-G		not specified	Uncertain significance (Apr 07, 2022)
17-20450102-T-G		not specified	Uncertain significance (Apr 25, 2023)
17-20451492-G-C		not specified	Uncertain significance (May 17, 2023)
17-20451518-G-A		not specified	Uncertain significance (Nov 15, 2021)
17-20451525-T-A		not specified	Uncertain significance (Nov 08, 2022)
17-20451527-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-20451537-A-T		not specified	Uncertain significance (Jan 03, 2024)
17-20451591-G-A		not specified	Uncertain significance (Jun 05, 2024)
17-20451593-G-C		not specified	Uncertain significance (Jun 02, 2023)
17-20451609-C-T		not specified	Uncertain significance (May 05, 2023)
17-20451816-G-A		not specified	Uncertain significance (Mar 21, 2023)
17-20451858-G-A		not specified	Uncertain significance (Mar 25, 2024)
17-20453019-A-G		not specified	Likely benign (Aug 28, 2023)
17-20453027-T-A		not specified	Uncertain significance (Jan 22, 2024)
17-20453027-T-C		not specified	Uncertain significance (Jun 22, 2023)
17-20453061-T-A			Likely benign (Nov 01, 2022)
17-20455392-G-A		not specified	Uncertain significance (Mar 18, 2024)
17-20456575-A-G		not specified	Uncertain significance (Dec 08, 2021)
17-20458186-G-T		not specified	Uncertain significance (Feb 28, 2023)
17-20458244-A-C		not specified	Uncertain significance (Jun 07, 2023)
17-20458263-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-20458298-A-G		not specified	Uncertain significance (Apr 01, 2022)
17-20458311-C-T		not specified	Uncertain significance (Oct 06, 2023)
17-20458344-T-C		not specified	Uncertain significance (Nov 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS9B	protein_coding	protein_coding	ENST00000324290	11	18145

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000844	0.788	125694	1	15	125710	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.541	154	174	0.885	0.0000102	2302
Missense in Polyphen		51	58.119	0.8775		722
Synonymous	0.439	64	68.6	0.933	0.00000442	670
Loss of Function	1.15	8	12.4	0.646	5.28e-7	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000223	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000951	0.0000792
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds galactosides. {ECO:0000250}.

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytosol
• Molecular function: protein binding;carbohydrate binding