M6PR

mannose-6-phosphate receptor, cation dependent, the group of MRH domain containing

Basic information

Region (hg38): 12:8940361-8949761

Links

ENSG00000003056

∙ NCBI:4074 ∙ OMIM:154540 ∙ HGNC:6752 ∙ Uniprot:P20645 ∙ 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 M6PR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the M6PR 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 clinvar			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in M6PR

This is a list of pathogenic ClinVar variants found in the M6PR region.

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

Position	Phenotype	Significance	ClinVar
12-8941823-T-C	not specified	Uncertain significance (Jul 13, 2022)	2301554
12-8941856-C-T	not specified	Uncertain significance (Jan 18, 2023)	2476194
12-8943507-C-T	not specified	Uncertain significance (Oct 14, 2021)	2255441
12-8943802-G-A	not specified	Uncertain significance (Mar 04, 2024)	3121819
12-8943884-C-T	not specified	Uncertain significance (Dec 10, 2024)	3541769
12-8945474-C-G	not specified	Uncertain significance (Jun 11, 2021)	2379035
12-8945484-T-C	not specified	Uncertain significance (Feb 14, 2023)	3121818
12-8945525-C-T	not specified	Uncertain significance (Jun 17, 2022)	2411703
12-8945576-C-T	not specified	Uncertain significance (Feb 17, 2022)	2355382
12-8945578-C-G	not specified	Uncertain significance (Sep 07, 2022)	2311409
12-8946233-T-C	not specified	Uncertain significance (Oct 27, 2023)	3121817
12-8946332-A-G	not specified	Uncertain significance (Aug 16, 2021)	2390389

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
M6PR	protein_coding	protein_coding	ENST00000000412	6	9593

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00922	0.980	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.979	121	155	0.779	0.00000828	1809
Missense in Polyphen		42	72.049	0.58294		797
Synonymous	1.05	47	57.1	0.823	0.00000275	543
Loss of Function	2.24	6	15.5	0.386	9.74e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000614	0.000612
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000264	0.000264
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transport of phosphorylated lysosomal enzymes from the Golgi complex and the cell surface to lysosomes. Lysosomal enzymes bearing phosphomannosyl residues bind specifically to mannose-6- phosphate receptors in the Golgi apparatus and the resulting receptor-ligand complex is transported to an acidic prelyosomal compartment where the low pH mediates the dissociation of the complex.;
Pathway: Phagosome - Homo sapiens (human);Lysosome - Homo sapiens (human);Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.790

Intolerance Scores

loftool: 0.620
rvis_EVS: -0.16
rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

pHI: 0.732
hipred: Y
hipred_score: 0.825
ghis: 0.690

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: M6pr
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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype;

Gene ontology

Biological process: protein targeting to lysosome;receptor-mediated endocytosis;endosome to lysosome transport;secretion of lysosomal enzymes;membrane organization
Cellular component: lysosomal membrane;endosome;late endosome;trans-Golgi network;plasma membrane;integral component of plasma membrane;membrane;transport vesicle;clathrin-coated vesicle membrane;retromer complex;trans-Golgi network membrane;perinuclear region of cytoplasm
Molecular function: transmembrane signaling receptor activity;protein binding;mannose binding;protein domain specific binding;retromer complex binding