LACTB2

lactamase beta 2, the group of MBL domain containing glyoxalase 2 subfamily

Basic information

Region (hg38): 8:70635317-70669185

Links

ENSG00000147592 ∙ NCBI:51110 ∙ OMIM:618921 ∙ HGNC:18512 ∙ Uniprot:Q53H82 ∙ 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 LACTB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LACTB2 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in LACTB2

This is a list of pathogenic ClinVar variants found in the LACTB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-70637868-G-A		not specified	Uncertain significance (Oct 05, 2023)
8-70638611-G-A		not specified	Uncertain significance (Mar 30, 2024)
8-70640957-C-G		not specified	Uncertain significance (May 15, 2024)
8-70640957-C-T		not specified	Likely benign (Jan 03, 2024)
8-70640984-C-T		not specified	Uncertain significance (Dec 05, 2022)
8-70640987-A-G		not specified	Uncertain significance (Sep 28, 2022)
8-70641008-T-A		not specified	Uncertain significance (Dec 30, 2023)
8-70644086-T-G		not specified	Uncertain significance (Apr 25, 2022)
8-70644227-C-T		not specified	Uncertain significance (Sep 22, 2022)
8-70657829-T-C		not specified	Uncertain significance (Jul 14, 2022)
8-70657873-T-C		not specified	Uncertain significance (Jul 20, 2022)
8-70661810-G-C		not specified	Uncertain significance (Jan 23, 2024)
8-70661850-C-A		not specified	Uncertain significance (Oct 04, 2022)
8-70669014-A-C		not specified	Uncertain significance (Dec 13, 2022)
8-70669093-G-C		not specified	Uncertain significance (Mar 21, 2024)
8-70669108-G-C		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LACTB2	protein_coding	protein_coding	ENST00000276590	7	33857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000369	0.837	125716	1	30	125747	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.433	130	145	0.899	0.00000676	1878
Missense in Polyphen		37	39.682	0.93241		497
Synonymous	0.729	44	50.6	0.870	0.00000228	536
Loss of Function	1.32	9	14.4	0.624	7.56e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000399	0.000395
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000220	0.000217
South Asian	0.000165	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endoribonuclease; cleaves preferentially 3' to purine- pyrimidine dinucleotide motifs in single-stranded RNA. The cleavage product contains a free 3' -OH group. Has no activity with double-stranded RNA or DNA. Required for normal mitochondrial function and cell viability. {ECO:0000269|PubMed:26826708}.

Recessive Scores

• pRec: 0.0908

Intolerance Scores

• loftool: 0.655
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.197
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.928

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lactb2
• Phenotype: growth/size/body region 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; 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); 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype

Gene ontology

• Biological process: RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: mitochondrial matrix
• Molecular function: single-stranded RNA binding;endoribonuclease activity;protein binding;zinc ion binding