MANEAL

mannosidase endo-alpha like, the group of Mannosidases endo-alpha

Basic information

Region (hg38): 1:37793847-37801137

Links

ENSG00000185090 ∙ NCBI:149175 ∙ ∙ HGNC:26452 ∙ Uniprot:Q5VSG8 ∙ 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 MANEAL gene.

• not_specified (62 variants)
• MANEAL-associated_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MANEAL gene is commonly pathogenic or not. These statistics are base on transcript: NM_001113482.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			58	2		60
nonsense						0
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	58	4	0

Highest pathogenic variant AF is 0.000002482967

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MANEAL	protein_coding	protein_coding	ENST00000373045	4	7336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00494	0.970	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.377	215	231	0.930	0.0000138	2926
Missense in Polyphen		67	77.104	0.86896		982
Synonymous	0.532	94	101	0.933	0.00000662	949
Loss of Function	1.96	6	13.9	0.432	6.04e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000210
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.0000544	0.0000544
Finnish	0.000328	0.000323
European (Non-Finnish)	0.0000445	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.000132	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.0998
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.698
• hipred: N
• hipred_score: 0.319
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.518

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Maneal
• Phenotype: hematopoietic system phenotype

Gene ontology

• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: alpha-mannosidase activity