LGALS16

galectin 16, the group of Galectins

Basic information

Region (hg38): 19:39655912-39660647

Links

ENSG00000249861 ∙ NCBI:148003 ∙ ∙ HGNC:40039 ∙ Uniprot:A8MUM7 ∙ 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 LGALS16 gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS16 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in LGALS16

This is a list of pathogenic ClinVar variants found in the LGALS16 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39657887-C-T		not specified	Uncertain significance (Dec 02, 2021)
19-39657925-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-39658464-G-A		not specified	Uncertain significance (Feb 10, 2023)
19-39658506-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-39658567-G-A		not specified	Uncertain significance (Oct 03, 2022)
19-39658641-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-39658644-A-G		not specified	Uncertain significance (Apr 22, 2022)
19-39658650-G-A		not specified	Uncertain significance (Nov 22, 2023)
19-39660417-T-C		not specified	Uncertain significance (Jul 17, 2023)
19-39660441-C-T		not specified	Uncertain significance (Mar 16, 2022)
19-39660458-A-C		not specified	Uncertain significance (Jan 19, 2024)
19-39660512-C-T		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS16	protein_coding	protein_coding	ENST00000392051	4	4754

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000100	0.368	125663	0	5	125668	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.163	77	81.1	0.949	0.00000480	904
Missense in Polyphen		23	21.612	1.0642		283
Synonymous	1.11	22	29.7	0.742	0.00000161	258
Loss of Function	0.0228	6	6.06	0.990	3.40e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds lactose with high affinity. Strong inducer of T- cell apoptosis. {ECO:0000269|PubMed:19497882}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Gene ontology

• Biological process: apoptotic process;positive regulation of T cell apoptotic process
• Cellular component: cellular_component
• Molecular function: lactose binding