MAN1A2

mannosidase alpha class 1A member 2, the group of Mannosidases alpha class 1

Basic information

Region (hg38): 1:117367448-117528872

Links

ENSG00000198162 ∙ NCBI:10905 ∙ OMIM:604345 ∙ HGNC:6822 ∙ Uniprot:O60476 ∙ 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 MAN1A2 gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAN1A2 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	11	0	0

Variants in MAN1A2

This is a list of pathogenic ClinVar variants found in the MAN1A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-117368190-A-G		not specified	Uncertain significance (Oct 20, 2023)
1-117368245-C-T		not specified	Uncertain significance (Aug 03, 2022)
1-117368295-A-C		not specified	Uncertain significance (Apr 25, 2023)
1-117368481-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-117402187-G-C		not specified	Uncertain significance (Apr 06, 2022)
1-117402199-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-117402200-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-117402284-G-A		not specified	Uncertain significance (Dec 14, 2022)
1-117414794-G-A		not specified	Uncertain significance (Aug 14, 2023)
1-117420608-A-G		not specified	Uncertain significance (Jul 26, 2022)
1-117442310-T-C		not specified	Uncertain significance (Jan 16, 2024)
1-117460507-G-T		not specified	Uncertain significance (Nov 17, 2022)
1-117460568-A-C		not specified	Uncertain significance (May 31, 2023)
1-117466336-T-G			Benign (May 02, 2018)
1-117493153-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-117496766-A-G		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAN1A2	protein_coding	protein_coding	ENST00000356554	13	161424

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00108	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	211	345	0.612	0.0000171	4185
Missense in Polyphen		26	93.945	0.27676		1164
Synonymous	0.104	117	118	0.988	0.00000542	1233
Loss of Function	4.84	3	33.0	0.0908	0.00000176	412

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maturation of Asn-linked oligosaccharides. Progressively trim alpha-1,2-linked mannose residues from Man(9)GlcNAc(2) to produce Man(5)GlcNAc(2).
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);N-Glycan biosynthesis - Homo sapiens (human);Vesicle-mediated transport;er associated degradation (erad) pathway;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;N-glycan trimming and elongation in the cis-Golgi;Progressive trimming of alpha-1,2-linked mannose residues from Man9/8/7GlcNAc2 to produce Man5GlcNAc2;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Intra-Golgi traffic;N-Glycan biosynthesis;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.213
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.509
• hipred: Y
• hipred_score: 0.688
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.528

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Man1a2
• Phenotype: respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein glycosylation;N-glycan processing;respiratory gaseous exchange;lung alveolus development;Golgi apparatus mannose trimming
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;membrane;integral component of membrane;extracellular exosome
• Molecular function: mannosyl-oligosaccharide 1,2-alpha-mannosidase activity;calcium ion binding