LGALS9C

protein-coding

galectin 9C, the group of Galectins

Gene summary

This gene was initially thought to represent a pseudogene of galectin 9; however, this transcript has good exon-intron structure and encodes a predicted protein of the same size as and highly similar to galectin 9. This gene is one of two similar loci on chromosome 17p similar to galectin 9 and now thought to be protein-encoding. This gene is the more telomeric gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001040078.3

Inheritance

—

ClinVar variants

U:57B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr17:18,476,737-18,494,945

External References & Databases

Ensembl (ENSG00000171916)

Transcript & Mutation Effects

hg38 • Region Span ~18.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LGALS9C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040078.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			53 clinvar	5 clinvar		58
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	57	6	0	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040078.3	RefSeq	NP_001035167.2	11	MANE Select
ENST00000328114.11	Ensembl	ENSP00000329932.6	11	MANE Select
NM_001438918.1	RefSeq	NP_001425847.1	11	Standard
NM_001438919.1	RefSeq	NP_001425848.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TYROBP Causal Network

Molecular Function

protein binding
carbohydrate binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328114
Coding exons: 11
Length: 18209
Individuals with no LoFs: 124899
Homozygous LoFs: 9
Heterozygous LoFs: 181
Defined: 125089
p: 0.000760

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.897	155	190	0.817	0.0000111	2302
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00049	0.00046	rare
Ashkenazi Jewish	0.00011	0.00010	rare
East Asian	0.00027	0.00027	rare
Finnish	0.00070	0.00060	rare
European (Non-Finnish)	0.0015	0.0013	notable
South Asian	0.00018	0.00013	rare
Other	0.00071	0.00066	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.915
RVIS EVS: -0.32
RVIS percentile EVS: 31.69

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0271

Gene Damage Prediction

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