LGSN

lengsin, lens protein with glutamine synthetase domain

Basic information

Region (hg38): 6:63275951-63319983

Previous symbols: [ "GLULD1" ]

Links

ENSG00000146166 ∙ NCBI:51557 ∙ OMIM:611470 ∙ HGNC:21016 ∙ Uniprot:Q5TDP6 ∙ 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 LGSN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGSN 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			30	2	1	33
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	1

Variants in LGSN

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

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

Position	Type	Phenotype	Significance	ClinVar
6-63280026-T-C		not specified	Uncertain significance (Oct 18, 2021)
6-63280040-A-T		not specified	Uncertain significance (Jan 26, 2023)
6-63280074-C-G		not specified	Uncertain significance (Aug 08, 2023)
6-63280077-A-T		not specified	Uncertain significance (Mar 28, 2024)
6-63280128-C-G		not specified	Uncertain significance (Jun 24, 2022)
6-63280128-C-T		not specified	Uncertain significance (Jun 28, 2022)
6-63280197-G-A		not specified	Uncertain significance (Apr 15, 2024)
6-63280206-G-C		not specified	Uncertain significance (Dec 11, 2023)
6-63280211-A-G		not specified	Uncertain significance (Feb 26, 2024)
6-63280226-T-C			Benign (Jul 13, 2018)
6-63280286-G-A		not specified	Uncertain significance (Jun 11, 2021)
6-63280340-C-T		not specified	Uncertain significance (Feb 16, 2023)
6-63280368-T-C		not specified	Uncertain significance (Dec 13, 2023)
6-63280399-C-G		not specified	Uncertain significance (Oct 03, 2022)
6-63280454-C-T		not specified	Uncertain significance (May 26, 2023)
6-63280466-G-A		not specified	Uncertain significance (Dec 17, 2021)
6-63280538-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-63280540-G-A		not specified	Likely benign (Dec 14, 2023)
6-63280553-C-T		not specified	Uncertain significance (Apr 19, 2023)
6-63280640-A-G		not specified	Uncertain significance (Jul 29, 2022)
6-63280786-C-A		not specified	Uncertain significance (May 31, 2023)
6-63280818-C-T		not specified	Uncertain significance (Oct 06, 2022)
6-63280848-G-C		not specified	Uncertain significance (May 17, 2023)
6-63280853-T-C		not specified	Uncertain significance (Jul 26, 2022)
6-63280875-A-T		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGSN	protein_coding	protein_coding	ENST00000370657	4	44027

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.59e-13	0.0145	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.555	297	271	1.09	0.0000133	3369
Missense in Polyphen		60	67.84	0.88443		829
Synonymous	-2.28	129	100	1.29	0.00000513	974
Loss of Function	-0.251	19	17.9	1.06	0.00000108	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000730	0.000730
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000831	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.000831	0.000816
South Asian	0.000360	0.000359
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a component of the cytoskeleton or as a chaperone for the reorganization of intermediate filament proteins during terminal differentiation in the lens. Does not seem to have enzymatic activity (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.321
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.47

Haploinsufficiency Scores

• pHI: 0.0693
• hipred: N
• hipred_score: 0.216

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0939

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgsn

Zebrafish Information Network

• Gene name: lgsn
• Affected structure: retina
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: glutamine biosynthetic process;nitrogen utilization
• Cellular component: plasma membrane;membrane
• Molecular function: glutamate-ammonia ligase activity