LMBRD2

LMBR1 domain containing 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 5:36098407-36151887

Links

ENSG00000164187 ∙ NCBI:92255 ∙ OMIM:619490 ∙ HGNC:25287 ∙ Uniprot:Q68DH5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with microcephaly and dysmorphic facies (Moderate), mode of inheritance: AD
• complex neurodevelopmental disorder (No Known Disease Relationship), mode of inheritance: AD
• developmental delay with variable neurologic and brain abnormalities (Moderate), mode of inheritance: AD
• developmental delay with variable neurologic and brain abnormalities (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental delay with variable neurologic and brain abnormalities	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic; Ophthalmologic	32820033

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMBRD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMBRD2 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					3	3
missense		4	42	3	1	50
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding						0
Total	0	4	45	3	4

Variants in LMBRD2

This is a list of pathogenic ClinVar variants found in the LMBRD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-36104058-A-C		Developmental delay with variable neurologic and brain abnormalities	Likely benign (Feb 02, 2022)
5-36105080-G-A		Inborn genetic diseases • LMBRD2-related disorder	Uncertain significance (Jun 10, 2022)
5-36105083-T-C		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
5-36105147-C-G		LMBRD2-related disorder	Uncertain significance (Mar 22, 2022)
5-36105149-A-G		LMBRD2-related disorder	Uncertain significance (Aug 14, 2023)
5-36105152-C-T		LMBRD2-related disorder	Likely benign (Oct 07, 2022)
5-36105153-G-A		LMBRD2-related disorder	Uncertain significance (Jun 05, 2024)
5-36108536-C-T		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
5-36108537-G-A		Inborn genetic diseases	Uncertain significance (Jun 10, 2024)
5-36108549-C-T		Inborn genetic diseases	Likely benign (May 15, 2024)
5-36108567-C-T		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
5-36108587-T-G			Uncertain significance (Apr 17, 2023)
5-36108599-G-C		Developmental delay with variable neurologic and brain abnormalities	Uncertain significance (Jul 22, 2023)
5-36108600-T-C			Uncertain significance (Feb 10, 2023)
5-36108623-T-C		Inborn genetic diseases	Uncertain significance (Mar 08, 2024)
5-36108639-C-G		Neurodevelopmental disorder	Uncertain significance (Jun 24, 2022)
5-36109940-C-T			Uncertain significance (Dec 17, 2023)
5-36109941-T-C		Developmental delay with variable neurologic and brain abnormalities	Uncertain significance (May 20, 2023)
5-36109977-G-C		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
5-36111188-A-C		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
5-36111194-A-C		Inborn genetic diseases	Uncertain significance (Oct 06, 2021)
5-36111253-C-G		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)
5-36111257-A-C		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
5-36114465-A-T			Uncertain significance (Oct 10, 2023)
5-36114496-G-C			Likely pathogenic (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMBRD2	protein_coding	protein_coding	ENST00000296603	17	53550

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000164	1.00	125713	0	33	125746	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	241	363	0.664	0.0000184	4574
Missense in Polyphen		81	150.93	0.53666		1912
Synonymous	0.849	108	120	0.901	0.00000577	1257
Loss of Function	3.81	14	40.0	0.350	0.00000205	514

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000917	0.0000907
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000665	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000207	0.000202
Middle Eastern	0.0000665	0.0000544
South Asian	0.000103	0.0000980
Other	0.000335	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.334
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.488
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.462

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmbrd2

Gene ontology

• Cellular component: membrane;integral component of membrane