LUM

lumican, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 12:91102629-91111494

Previous symbols: [ "LDC" ]

Links

ENSG00000139329 ∙ NCBI:4060 ∙ OMIM:600616 ∙ HGNC:6724 ∙ Uniprot:P51884 ∙ 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 LUM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LUM 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				3	2	5
missense			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	10	5	5

Variants in LUM

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

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

Position	Type	Phenotype	Significance	ClinVar
12-91104209-T-C		not specified	Uncertain significance (Mar 07, 2023)
12-91104290-G-T		not specified	Uncertain significance (May 16, 2023)
12-91104422-C-T			Benign (Jun 20, 2021)
12-91104522-T-A			Benign (Jun 20, 2021)
12-91108131-G-A		LUM-related disorder	Benign (Jun 26, 2019)
12-91108169-T-C		not specified	Uncertain significance (Feb 17, 2022)
12-91108389-G-A		LUM-related disorder	Likely benign (Jul 10, 2019)
12-91108447-G-A		not specified	Uncertain significance (May 17, 2023)
12-91108473-A-G		LUM-related disorder	Benign (Jun 09, 2021)
12-91108561-T-A		not specified	Likely benign (Dec 20, 2023)
12-91108585-A-C		not specified	Uncertain significance (Mar 04, 2024)
12-91108680-G-A		LUM-related disorder	Likely benign (Mar 06, 2019)
12-91108729-T-G		not specified	Uncertain significance (Jan 27, 2022)
12-91108733-C-G		not specified	Uncertain significance (Feb 06, 2023)
12-91108738-A-G		not specified	Uncertain significance (Dec 21, 2022)
12-91108758-C-T		LUM-related disorder	Likely benign (May 02, 2019)
12-91108814-G-T		not specified	Uncertain significance (Mar 06, 2023)
12-91108930-C-T		not specified	Uncertain significance (May 09, 2023)
12-91108955-A-G		not specified	Likely benign (Aug 17, 2021)
12-91109269-C-CTT			Benign (Jun 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LUM	protein_coding	protein_coding	ENST00000266718	2	9203

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0770	0.877	125704	0	9	125713	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	113	174	0.648	0.00000874	2223
Missense in Polyphen		25	60.902	0.41049		792
Synonymous	0.525	64	69.6	0.920	0.00000338	666
Loss of Function	1.70	3	8.27	0.363	3.46e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000704
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Proteoglycans in cancer - Homo sapiens (human);Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Integrin cell surface interactions;Glycosaminoglycan metabolism;Extracellular matrix organization;Metabolism;Integrin;ECM proteoglycans (Consensus)

Recessive Scores

• pRec: 0.293

Intolerance Scores

• loftool: 0.366
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.914
• hipred: Y
• hipred_score: 0.573
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.737

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lum
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; skeleton phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: lum
• Affected structure: sclera
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: visual perception;response to organic cyclic compound;keratan sulfate biosynthetic process;extracellular matrix organization;collagen fibril organization;positive regulation of transforming growth factor beta1 production;keratan sulfate catabolic process;positive regulation of transcription by RNA polymerase II;cartilage development;response to growth factor
• Cellular component: extracellular region;fibrillar collagen trimer;extracellular space;Golgi lumen;extracellular matrix;lysosomal lumen;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: extracellular matrix structural constituent;protein binding;collagen binding;extracellular matrix structural constituent conferring compression resistance