MPP4

MAGUK p55 scaffold protein 4, the group of PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 2:201644870-201698694

Previous symbols: [ "DLG6" ]

Links

ENSG00000082126 ∙ NCBI:58538 ∙ OMIM:606575 ∙ HGNC:13680 ∙ Uniprot:Q96JB8 ∙ 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 MPP4 gene.

• not_specified (88 variants)
• not_provided (2 variants)
• Strabismus (1 variants)
• Generalized_hypotonia (1 variants)
• Wide_nasal_bridge (1 variants)
• High_palate (1 variants)
• Seizure (1 variants)
• Global_developmental_delay (1 variants)
• Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPP4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033066.3. 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				2		2
missense	1		85	2		88
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	1	0	85	5	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPP4	protein_coding	protein_coding	ENST00000409474	21	53825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.42e-18	0.124	124456	0	190	124646	0.000762

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.454	316	340	0.931	0.0000180	4175
Missense in Polyphen		105	117.55	0.8932		1384
Synonymous	0.530	116	123	0.939	0.00000702	1141
Loss of Function	1.26	32	40.7	0.786	0.00000203	479

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00457	0.00456
Ashkenazi Jewish	0.000613	0.000596
East Asian	0.000279	0.000278
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000613	0.000575
Middle Eastern	0.000279	0.000278
South Asian	0.000653	0.000588
Other	0.000671	0.000661

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in retinal photoreceptors development. {ECO:0000250}.
• Pathway: Tight junction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0908

Intolerance Scores

• loftool: 0.693
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.57

Haploinsufficiency Scores

• pHI: 0.853
• hipred: N
• hipred_score: 0.487
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.453

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpp4
• Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: biological_process;protein localization to synapse
• Cellular component: cytosol;cell-cell adherens junction;actin cytoskeleton;protein-containing complex
• Molecular function: protein binding