MAN1A2

protein-coding

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

Gene summary

Alpha-mannosidases function at different stages of N-glycan maturation in mammalian cells. See MAN2A1 (MIM 154582) for general information.[supplied by OMIM, Mar 2008]

MANE transcript

NM_006699.5

Inheritance

—

ClinVar variants

U:54B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr1:117,367,449-117,528,872

External References & Databases

Ensembl (ENSG00000198162)

Transcript & Mutation Effects

hg38 • Region Span ~161.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAN1A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006699.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			49 clinvar			49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	54	0	1	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006699.5	RefSeq	NP_006690.1	13	MANE Select
ENST00000356554.7	Ensembl	ENSP00000348959.3	13	MANE Select
ENST00000421535.5	Ensembl	ENSP00000396362.1	5	Standard
ENST00000422329.1	Ensembl	ENSP00000402416.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein processing in endoplasmic reticulum - Homo sapiens (human)
N-Glycan biosynthesis - Homo sapiens (human)
Vesicle-mediated transport
er associated degradation (erad) pathway
Membrane Trafficking

Biological Process

protein glycosylation
N-glycan processing
respiratory gaseous exchange
lung alveolus development
Golgi apparatus mannose trimming

Molecular Function

mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
calcium ion binding

Cellular Component

Golgi membrane
endoplasmic reticulum
Golgi apparatus
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356554
Coding exons: 13
Length: 161424
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125747
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.56	211	345	0.612	0.0000171	4185
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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).;

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.213
RVIS EVS: 0.02
RVIS percentile EVS: 55.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.528

Gene Damage Prediction

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