LGALS9C

galectin 9C, the group of Galectins

Basic information

Region (hg38): 17:18476737-18494945

Links

ENSG00000171916 ∙ NCBI:654346 ∙ ∙ HGNC:33874 ∙ Uniprot:Q6DKI2 ∙ 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 LGALS9C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS9C 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	2		23
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	0

Variants in LGALS9C

This is a list of pathogenic ClinVar variants found in the LGALS9C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18476867-G-A		not specified	Likely benign (May 10, 2024)
17-18476876-G-C		not specified	Likely benign (Mar 22, 2023)
17-18476885-C-A		not specified	Uncertain significance (Nov 18, 2023)
17-18485945-A-C		not specified	Uncertain significance (Jan 30, 2024)
17-18485954-C-T		not specified	Uncertain significance (Nov 10, 2022)
17-18485969-A-T		not specified	Uncertain significance (Nov 06, 2023)
17-18486005-A-G		not specified	Uncertain significance (Jan 02, 2024)
17-18486007-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-18486019-G-A		not specified	Uncertain significance (Mar 29, 2024)
17-18486088-G-A		not specified	Uncertain significance (Dec 27, 2023)
17-18486106-T-G		not specified	Uncertain significance (Jun 11, 2024)
17-18487665-C-T		not specified	Likely benign (Sep 27, 2022)
17-18487709-C-A		not specified	Uncertain significance (Mar 06, 2023)
17-18487709-CA-C			Likely benign (Nov 01, 2022)
17-18488948-G-T		not specified	Uncertain significance (Aug 30, 2022)
17-18488984-C-T		not specified	Uncertain significance (Oct 02, 2023)
17-18488998-G-A		not specified	Uncertain significance (May 31, 2023)
17-18492524-C-T		not specified	Uncertain significance (Mar 21, 2023)
17-18492747-C-G		not specified	Uncertain significance (Jun 02, 2023)
17-18492754-T-G		not specified	Uncertain significance (Sep 01, 2021)
17-18492758-G-A		not specified	Uncertain significance (Jun 29, 2023)
17-18492839-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-18494221-G-T		not specified	Uncertain significance (Oct 05, 2023)
17-18494260-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-18494275-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS9C	protein_coding	protein_coding	ENST00000328114	11	18209

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.20e-9	0.136	124899	9	181	125089	0.000760

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.897	155	190	0.817	0.0000111	2302
Missense in Polyphen		45	63.999	0.70313		759
Synonymous	0.922	65	75.2	0.865	0.00000488	659
Loss of Function	0.168	13	13.7	0.951	5.82e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000682	0.000675
Ashkenazi Jewish	0.000108	0.0000995
East Asian	0.000273	0.000272
Finnish	0.000700	0.000604
European (Non-Finnish)	0.00151	0.00128
Middle Eastern	0.000273	0.000272
South Asian	0.000181	0.000131
Other	0.000715	0.000656

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds galactosides. {ECO:0000250}.
• Pathway: TYROBP Causal Network (Consensus)

Intolerance Scores

• loftool: 0.915
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0271

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