MPP2

MAGUK p55 scaffold protein 2, the group of PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 17:43875357-43909711

Previous symbols: [ "DLG2" ]

Links

ENSG00000108852 ∙ NCBI:4355 ∙ OMIM:600723 ∙ HGNC:7220 ∙ Uniprot:Q14168 ∙ 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 MPP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPP2 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in MPP2

This is a list of pathogenic ClinVar variants found in the MPP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-43877937-C-T		not specified	Uncertain significance (Mar 31, 2024)
17-43877938-G-A		not specified	Uncertain significance (Aug 22, 2023)
17-43877967-C-T		not specified	Uncertain significance (Jan 03, 2022)
17-43879309-G-T		not specified	Uncertain significance (Aug 22, 2023)
17-43879379-C-T		not specified	Uncertain significance (Aug 16, 2021)
17-43879822-A-G		not specified	Uncertain significance (Aug 10, 2021)
17-43879841-C-T		not specified	Uncertain significance (Apr 06, 2023)
17-43879904-C-T		not specified	Likely benign (Sep 22, 2023)
17-43879925-G-A		not specified	Uncertain significance (Dec 05, 2022)
17-43879955-G-A		not specified	Uncertain significance (Mar 23, 2023)
17-43880793-G-A		not specified	Uncertain significance (Oct 16, 2023)
17-43880796-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-43880810-C-T		not specified	Uncertain significance (Jan 09, 2024)
17-43881147-C-T		not specified	Uncertain significance (Dec 20, 2021)
17-43881247-A-G		not specified	Uncertain significance (Feb 21, 2024)
17-43882288-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-43882352-G-A		not specified	Uncertain significance (Sep 30, 2021)
17-43882371-G-A			Likely benign (Jun 01, 2022)
17-43882373-G-A		not specified	Uncertain significance (Mar 01, 2023)
17-43882955-G-A		not specified	Uncertain significance (Dec 08, 2023)
17-43883040-T-G		not specified	Uncertain significance (Jul 13, 2021)
17-43883270-G-A		not specified	Uncertain significance (Jan 23, 2023)
17-43883280-G-A		not specified	Uncertain significance (May 13, 2024)
17-43898290-T-C		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPP2	protein_coding	protein_coding	ENST00000269095	12	34344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.88e-7	0.982	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	289	371	0.779	0.0000253	3558
Missense in Polyphen		112	154.75	0.72374		1563
Synonymous	0.314	150	155	0.968	0.0000108	1146
Loss of Function	2.20	15	27.5	0.546	0.00000151	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000422
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000341	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Postsynaptic MAGUK scaffold protein that links CADM1 cell adhesion molecules to core components of the postsynaptic density (By similarity). In CA1 pyramidal neurons, required for synaptic KCNN2-containing channel function and long-term potentiation expression (By similarity). Seems to negatively regulate SRC function in epithelial cells (PubMed:19665017). {ECO:0000250|UniProtKB:D3ZAA9, ECO:0000250|UniProtKB:Q9WV34, ECO:0000269|PubMed:19665017}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.612
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8

Haploinsufficiency Scores

• pHI: 0.589
• hipred: Y
• hipred_score: 0.658
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.122

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpp2

Gene ontology

• Biological process: protein homooligomerization;excitatory postsynaptic potential;long-term synaptic potentiation
• Cellular component: cytoplasm;cytoskeleton;postsynaptic density;dendrite membrane;dendritic spine membrane;dendritic spine;dendritic shaft
• Molecular function: protein binding