LACTB

lactamase beta, the group of Serine beta lactamase family

Basic information

Region (hg38): 15:63121833-63142061

Previous symbols: [ "MRPL56" ]

Links

ENSG00000103642 ∙ NCBI:114294 ∙ OMIM:608440 ∙ HGNC:16468 ∙ Uniprot:P83111 ∙ 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 LACTB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LACTB 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					1	1
missense			32		2	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	32	0	3

Variants in LACTB

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

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

Position	Type	Phenotype	Significance	ClinVar
15-63121878-C-T		not specified	Uncertain significance (Feb 13, 2024)
15-63121917-G-A			Benign (May 24, 2018)
15-63121917-G-C		Abnormality of neuronal migration	Benign (Oct 31, 2014)
15-63121921-G-C		not specified	Uncertain significance (Aug 23, 2021)
15-63121944-C-T			Benign (May 24, 2018)
15-63122022-G-T		not specified	Uncertain significance (Jun 10, 2024)
15-63122055-G-C		not specified	Uncertain significance (Jan 17, 2024)
15-63122056-G-T		not specified	Uncertain significance (Aug 30, 2022)
15-63122077-C-T		not specified	Uncertain significance (Feb 21, 2024)
15-63122140-C-G		not specified	Uncertain significance (Jun 02, 2023)
15-63122148-C-A		not specified	Uncertain significance (Jan 31, 2024)
15-63122195-C-G		not specified	Uncertain significance (May 31, 2023)
15-63122654-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-63126874-A-T		not specified	Uncertain significance (Nov 22, 2022)
15-63126905-G-C		not specified	Uncertain significance (Jan 10, 2022)
15-63126954-C-T		not specified	Uncertain significance (Oct 16, 2023)
15-63126963-T-G		not specified	Uncertain significance (Nov 01, 2021)
15-63127003-A-C		not specified	Uncertain significance (Feb 15, 2023)
15-63127346-C-A			Benign (Apr 04, 2018)
15-63127419-A-G		not specified	Uncertain significance (Mar 28, 2023)
15-63127543-A-C		not specified	Uncertain significance (Mar 11, 2024)
15-63127547-G-C		not specified	Likely benign (Apr 08, 2024)
15-63127564-G-A		not specified	Uncertain significance (Jul 14, 2021)
15-63127641-A-G		not specified	Uncertain significance (Dec 06, 2023)
15-63127641-A-T		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LACTB	protein_coding	protein_coding	ENST00000261893	6	20262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000198	0.894	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	207	265	0.782	0.0000131	3499
Missense in Polyphen		67	93.288	0.7182		1123
Synonymous	1.43	81	99.1	0.817	0.00000510	1063
Loss of Function	1.60	12	19.6	0.611	9.12e-7	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000333
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000282	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000900	0.0000879
Middle Eastern	0.000282	0.000272
South Asian	0.0000721	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial serine protease that acts as a regulator of mitochondrial lipid metabolism (PubMed:28329758). Acts by decreasing protein levels of PISD, a mitochondrial enzyme that converts phosphatidylserine (PtdSer) to phosphatidylethanolamine (PtdEtn), thereby affecting mitochondrial lipid metabolism (PubMed:28329758). It is unclear whether it acts directly by mediating proteolysis of PISD or by mediating proteolysis of another lipid metabolism protein (PubMed:28329758). Acts as a tumor suppressor that has the ability to inhibit proliferation of multiple types of breast cancer cells: probably by promoting decreased levels of PISD, thereby affecting mitochondrial lipid metabolism (PubMed:28329758). {ECO:0000269|PubMed:28329758}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.464
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.379
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0483

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lactb

Gene ontology

• Biological process: proteolysis;lipid metabolic process;regulation of lipid metabolic process
• Cellular component: mitochondrion;cytosol
• Molecular function: peptidase activity;identical protein binding