LALBA

lactalbumin alpha, the group of Lysozymes, c-type

Basic information

Region (hg38): 12:48567684-48570066

Links

ENSG00000167531 ∙ NCBI:3906 ∙ OMIM:149750 ∙ HGNC:6480 ∙ Uniprot:P00709 ∙ 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 LALBA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LALBA 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in LALBA

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

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

Position	Type	Phenotype	Significance	ClinVar
12-48568559-A-G		not specified	Uncertain significance (Jun 13, 2022)
12-48569106-T-C		not specified	Uncertain significance (Feb 13, 2024)
12-48569130-T-C		not specified	Uncertain significance (Nov 28, 2023)
12-48569174-G-A		not specified	Uncertain significance (Dec 14, 2022)
12-48569177-C-T		not specified	Uncertain significance (Mar 24, 2023)
12-48569184-T-C		not specified	Uncertain significance (Feb 11, 2022)
12-48569920-A-G		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LALBA	protein_coding	protein_coding	ENST00000301046	4	2383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.460	0.516	124335	0	1	124336	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.788	53	71.8	0.738	0.00000318	938
Missense in Polyphen		9	22.236	0.40475		313
Synonymous	0.136	27	27.9	0.967	0.00000133	248
Loss of Function	1.81	1	5.65	0.177	2.37e-7	74

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)	0.00000888	0.00000888
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of lactose synthase, changes the substrate specificity of galactosyltransferase in the mammary gland making glucose a good acceptor substrate for this enzyme. This enables LS to synthesize lactose, the major carbohydrate component of milk. In other tissues, galactosyltransferase transfers galactose onto the N-acetylglucosamine of the oligosaccharide chains in glycoproteins.
• Pathway: Galactose metabolism - Homo sapiens (human);GLUT-1 deficiency syndrome;Congenital disorder of glycosylation CDG-IId;Lactose Synthesis;Metabolism of carbohydrates;Metabolism;Lactose synthesis;Galactose metabolism (Consensus)

Recessive Scores

• pRec: 0.201

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.195

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lalba
• 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); endocrine/exocrine gland phenotype; normal phenotype

Gene ontology

• Biological process: lactose biosynthetic process;apoptotic process;signal transduction;cell-cell signaling;defense response to bacterium;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium
• Cellular component: Golgi membrane;extracellular space;Golgi lumen
• Molecular function: lactose synthase activity;calcium ion binding