LACC1

laccase domain containing 1

Basic information

Region (hg38): 13:43879283-43893932

Previous symbols: [ "C13orf31" ]

Links

ENSG00000179630 ∙ NCBI:144811 ∙ OMIM:613409 ∙ HGNC:26789 ∙ Uniprot:Q8IV20 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• juvenile arthritis due to defect in LACC1 (Limited), mode of inheritance: AR
• juvenile arthritis due to defect in LACC1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Juvenile arthritis	AR	Allergy/Immunology/Infectious; Oncologic	Individuals have been described as benefiting from specific medications (with non-efficacy of other medications), and knowledge may help with medication selection; The condition may involve increased risk of malignancy, and awareness may allow prompt diagnosis and management; BMT has been described	Allergy/Immunology/Infectious; Oncologic	25220867; 27881174; 29717096; 30872671

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LACC1 gene.

• Inborn genetic diseases (13 variants)
• not provided (9 variants)
• Juvenile arthritis due to defect in LACC1 (5 variants)
• Leprosy, susceptibility to, 1 (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LACC1 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				2		2
missense		1	15	2	2	20
nonsense						0
start loss						0
frameshift	2					2
inframe indel		1				1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	2	2	15	4	2

Variants in LACC1

This is a list of pathogenic ClinVar variants found in the LACC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-43880988-G-A		Juvenile arthritis due to defect in LACC1	Pathogenic (Feb 29, 2020)
13-43881097-A-G			Benign/Likely benign (Jun 01, 2023)
13-43881098-A-G		Inborn genetic diseases	Uncertain significance (Nov 17, 2023)
13-43881104-A-C		Inborn genetic diseases	Uncertain significance (Oct 06, 2022)
13-43881111-CTG-C		Juvenile arthritis due to defect in LACC1	Pathogenic (Nov 30, 2021)
13-43881157-C-A		Inborn genetic diseases	Uncertain significance (Apr 17, 2023)
13-43881160-G-C		Inborn genetic diseases	Uncertain significance (Mar 07, 2023)
13-43881199-C-A		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
13-43881238-G-A		Inborn genetic diseases	Uncertain significance (Oct 06, 2021)
13-43881250-T-TATACC		Juvenile arthritis due to defect in LACC1	Likely pathogenic (Sep 10, 2020)
13-43881274-GA-G			Pathogenic (Jun 30, 2022)
13-43881307-C-G			Likely benign (Apr 01, 2022)
13-43881344-A-C			Uncertain significance (Oct 01, 2022)
13-43881344-A-G		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
13-43881408-G-A			Likely benign (May 19, 2018)
13-43881422-C-A		Inborn genetic diseases	Uncertain significance (Apr 08, 2022)
13-43881422-C-G		Inborn genetic diseases	Uncertain significance (Jul 15, 2021)
13-43881467-A-C		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
13-43881476-T-G		Inborn genetic diseases	Uncertain significance (Dec 19, 2023)
13-43881488-T-C		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
13-43881490-A-G		Inborn genetic diseases	Uncertain significance (Apr 22, 2022)
13-43881536-C-G		Inborn genetic diseases	Uncertain significance (Dec 16, 2021)
13-43882311-G-A		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
13-43882313-A-G		Inborn genetic diseases	Uncertain significance (Dec 07, 2023)
13-43882356-G-A		Inborn genetic diseases	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LACC1	protein_coding	protein_coding	ENST00000441843	5	14649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000117	0.831	125696	0	37	125733	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	157	226	0.693	0.0000107	2854
Missense in Polyphen		30	57.459	0.52212		731
Synonymous	0.234	74	76.6	0.966	0.00000369	819
Loss of Function	1.35	10	15.8	0.634	8.24e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.00	0.00
Finnish	0.000418	0.000416
European (Non-Finnish)	0.0000974	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Central regulator of the metabolic function and bioenergetic state of macrophages. In macrophages, promotes flux through de novo lipogenesis to concomitantly drive high levels of both fatty-acid oxidation and glycolysis. {ECO:0000250|UniProtKB:Q8BZT9}.
• Disease: DISEASE: Rheumatoid arthritis systemic juvenile (RASJ) [MIM:604302]: An inflammatory articular disorder with systemic- onset beginning before the age of 16. It represents a subgroup of juvenile arthritis associated with severe extraarticular features and occasionally fatal complications. During active phases of the disorder, patients display a typical daily spiking fever, an evanescent macular rash, lymphadenopathy, hepatosplenomegaly, serositis, myalgia and arthritis. {ECO:0000269|PubMed:25220867}. Note=The gene represented in this entry may be involved in disease pathogenesis.

Recessive Scores

• pRec: 0.0899

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.261
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lacc1
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Cellular component: peroxisome
• Molecular function: copper ion binding;protein binding