MANEA

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

Basic information

Region (hg38): 6:95577485-95609470

Links

ENSG00000172469 ∙ NCBI:79694 ∙ OMIM:612327 ∙ HGNC:21072 ∙ Uniprot:Q5SRI9 ∙ 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 MANEA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MANEA 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			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	0

Variants in MANEA

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

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

Position	Type	Phenotype	Significance	ClinVar
6-95586453-G-A		not specified	Uncertain significance (Jan 03, 2024)
6-95586485-A-G		not specified	Uncertain significance (Apr 24, 2024)
6-95586513-G-A		not specified	Uncertain significance (Jun 26, 2023)
6-95586539-G-T		not specified	Uncertain significance (Jun 17, 2024)
6-95586552-C-T		not specified	Uncertain significance (Oct 04, 2022)
6-95586641-A-G		not specified	Uncertain significance (Oct 03, 2023)
6-95586668-A-C		not specified	Uncertain significance (Jan 10, 2022)
6-95586672-G-C		not specified	Uncertain significance (Mar 02, 2023)
6-95586683-A-C		not specified	Uncertain significance (Oct 03, 2022)
6-95586795-A-T		not specified	Uncertain significance (Feb 27, 2024)
6-95586804-A-G		not specified	Uncertain significance (Feb 28, 2023)
6-95586837-C-G		not specified	Uncertain significance (Nov 21, 2022)
6-95586858-C-T		not specified	Uncertain significance (Nov 10, 2022)
6-95586870-A-T		not specified	Uncertain significance (Dec 17, 2023)
6-95586871-C-G		not specified	Uncertain significance (Sep 26, 2023)
6-95586888-T-C		not specified	Uncertain significance (Jan 23, 2024)
6-95586894-C-T		not specified	Uncertain significance (Dec 20, 2023)
6-95586930-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-95586941-G-C		not specified	Uncertain significance (Feb 27, 2023)
6-95586974-G-T		not specified	Uncertain significance (Nov 09, 2023)
6-95596785-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-95604840-T-G		not specified	Uncertain significance (May 26, 2024)
6-95604872-A-G		not specified	Uncertain significance (Jun 02, 2024)
6-95604873-T-C		not specified	Uncertain significance (Dec 02, 2022)
6-95605783-C-G		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MANEA	protein_coding	protein_coding	ENST00000358812	4	31915

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000523	0.974	125715	0	31	125746	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00627	248	248	1.00	0.0000127	3044
Missense in Polyphen		101	108.41	0.93163		1336
Synonymous	-0.199	87	84.7	1.03	0.00000399	872
Loss of Function	1.97	8	16.7	0.479	8.86e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.000555	0.000555
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;N-glycan trimming and elongation in the cis-Golgi;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.227
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.475
• hipred: N
• hipred_score: 0.248
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Manea

Gene ontology

• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: alpha-mannosidase activity;glycoprotein endo-alpha-1,2-mannosidase activity