PMM1

phosphomannomutase 1, the group of HAD Asp-based non-protein phosphatases

Basic information

Region (hg38): 22:41576900-41589871

Links

ENSG00000100417 ∙ NCBI:5372 ∙ OMIM:601786 ∙ HGNC:9114 ∙ Uniprot:Q92871 ∙ 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 PMM1 gene.

• not_specified (37 variants)
• not_provided (1 variants)
• Global_developmental_delay,_absent_or_hypoplastic_corpus_callosum,_and_dysmorphic_facies (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PMM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002676.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense		1	37			38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	37	1	0

Highest pathogenic variant AF is 6.8439897e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PMM1	protein_coding	protein_coding	ENST00000216259	8	12997

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000166	0.668	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.840	137	168	0.817	0.0000106	1721
Missense in Polyphen		40	68.615	0.58297		643
Synonymous	0.123	74	75.4	0.982	0.00000533	506
Loss of Function	1.07	11	15.5	0.708	9.28e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000737	0.000736
Ashkenazi Jewish	0.00	0.00
East Asian	0.000986	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000986	0.000979
South Asian	0.000230	0.000229
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions. In addition, may be responsible for the degradation of glucose-1,6-bisphosphate in ischemic brain. {ECO:0000269|PubMed:16540464}.
• Pathway: Fructose and mannose metabolism - Homo sapiens (human);Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Fructose intolerance, hereditary;Fructose and Mannose Degradation;Fructosuria;Fructose Mannose metabolism;Post-translational protein modification;Metabolism of proteins;Synthesis of GDP-mannose;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;GDP-mannose biosynthesis (Consensus)

Recessive Scores

• pRec: 0.233

Intolerance Scores

• loftool: 0.321
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.248
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pmm1
• Phenotype: normal phenotype

Gene ontology

• Biological process: mannose metabolic process;protein N-linked glycosylation;GDP-mannose biosynthetic process;protein targeting to ER;cellular response to leukemia inhibitory factor
• Cellular component: cytosol;neuronal cell body
• Molecular function: phosphomannomutase activity;protein binding;metal ion binding