LAMB4

laminin subunit beta 4, the group of Laminin subunits

Basic information

Region (hg38): 7:108023547-108130361

Links

ENSG00000091128 ∙ NCBI:22798 ∙ OMIM:616380 ∙ HGNC:6491 ∙ Uniprot:A4D0S4 ∙ 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 LAMB4 gene.

• Inborn genetic diseases (68 variants)
• not provided (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAMB4 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	11	13
missense			64	5	2	71
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region				1	3	4
non coding						0
Total	0	0	64	7	15

Variants in LAMB4

This is a list of pathogenic ClinVar variants found in the LAMB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-108024059-AT-A			Benign (Dec 31, 2019)
7-108024092-T-C		not specified	Uncertain significance (Nov 18, 2022)
7-108029156-C-T		not specified	Likely benign (Sep 28, 2022)
7-108029180-T-C		not specified	Uncertain significance (Feb 28, 2024)
7-108030825-T-C		not specified	Uncertain significance (Jun 22, 2023)
7-108030844-C-G		not specified	Uncertain significance (Oct 06, 2021)
7-108030900-A-G		not specified	Uncertain significance (Apr 06, 2022)
7-108030915-T-C		not specified	Uncertain significance (Jun 18, 2021)
7-108034216-C-T		not specified	Uncertain significance (Sep 14, 2023)
7-108034226-T-C		not specified	Uncertain significance (Aug 08, 2023)
7-108034245-G-A		not specified	Uncertain significance (Apr 25, 2023)
7-108034265-G-T		not specified	Uncertain significance (Dec 20, 2023)
7-108034290-G-T		not specified	Uncertain significance (Jun 28, 2022)
7-108037395-C-T		not specified	Uncertain significance (Dec 28, 2022)
7-108037457-G-A		not specified	Uncertain significance (Jun 24, 2022)
7-108037575-C-G		not specified	Uncertain significance (Aug 17, 2022)
7-108043770-C-T		not specified	Uncertain significance (Mar 29, 2022)
7-108043779-T-G		not specified	Uncertain significance (Aug 15, 2023)
7-108043829-C-A			Benign (Dec 31, 2019)
7-108047924-C-T		not specified	Uncertain significance (Sep 22, 2023)
7-108047929-C-G		not specified	Uncertain significance (Oct 22, 2021)
7-108047994-G-A		not specified	Uncertain significance (Jun 03, 2022)
7-108047997-T-G		not specified	Uncertain significance (Aug 26, 2022)
7-108048015-C-T		not specified	Likely benign (Feb 12, 2024)
7-108048050-G-T		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAMB4	protein_coding	protein_coding	ENST00000388781	33	106809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.61e-42	0.000286	125256	6	486	125748	0.00196

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.146	974	961	1.01	0.0000518	11554
Missense in Polyphen		273	282.06	0.96787		3526
Synonymous	1.29	327	358	0.913	0.0000203	3272
Loss of Function	1.48	73	88.0	0.830	0.00000444	1106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0186	0.0183
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.00138	0.00136
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.000974	0.000959
Middle Eastern	0.00138	0.00136
South Asian	0.00137	0.00121
Other	0.000661	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);PI3K-Akt Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.261

Intolerance Scores

• loftool: 0.899
• rvis_EVS: -1.55
• rvis_percentile_EVS: 3.24

Haploinsufficiency Scores

• pHI: 0.0969
• hipred: N
• hipred_score: 0.144
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.353

Gene Damage Prediction

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

Gene ontology

• Biological process: cell adhesion
• Cellular component: basement membrane