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.

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.

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				1		1
missense			33	1		34
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	33	2	0

Variants in MANEAL

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

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

Position	Type	Phenotype	Significance	ClinVar
1-37794204-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-37794303-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-37794364-C-A		not specified	Uncertain significance (Jan 23, 2023)
1-37794382-C-G		not specified	Uncertain significance (Dec 14, 2021)
1-37794418-A-C		not specified	Likely benign (Oct 06, 2021)
1-37794445-C-A		not specified	Uncertain significance (Sep 14, 2021)
1-37794454-C-T		not specified	Uncertain significance (May 24, 2024)
1-37794480-C-A		not specified	Likely benign (Jun 18, 2024)
1-37794487-A-T		not specified	Uncertain significance (May 20, 2024)
1-37794534-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-37794547-A-G		not specified	Uncertain significance (Aug 11, 2022)
1-37794581-G-T		not specified	Uncertain significance (Aug 21, 2023)
1-37794622-G-GC		MANEAL-associated disorder	Likely pathogenic (Jan 16, 2020)
1-37794687-G-C		not specified	Uncertain significance (Jul 19, 2022)
1-37795801-C-T		not specified	Likely benign (May 26, 2023)
1-37795821-A-G		not specified	Uncertain significance (Dec 28, 2022)
1-37795832-C-G		not specified	Uncertain significance (Jun 22, 2023)
1-37796793-A-G		not specified	Uncertain significance (May 20, 2024)
1-37799571-G-C		not specified	Uncertain significance (Oct 02, 2023)
1-37799577-C-T		not specified	Uncertain significance (Nov 07, 2023)
1-37799578-A-G		not specified	Uncertain significance (Oct 20, 2023)
1-37799592-C-T		not specified	Uncertain significance (Feb 10, 2023)
1-37799635-T-A		not specified	Uncertain significance (Feb 28, 2023)
1-37799670-G-T		not specified	Uncertain significance (Mar 29, 2023)
1-37799713-C-T		not specified	Uncertain significance (May 25, 2022)

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