MPP3

MAGUK p55 scaffold protein 3, the group of PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 17:43800799-43833170

Previous symbols: [ "DLG3" ]

Links

ENSG00000161647 ∙ NCBI:4356 ∙ OMIM:601114 ∙ HGNC:7221 ∙ Uniprot:Q13368 ∙ 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 MPP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPP3 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in MPP3

This is a list of pathogenic ClinVar variants found in the MPP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-43801788-A-T		not specified	Uncertain significance (Nov 17, 2023)
17-43801831-C-T		not specified	Likely benign (May 27, 2022)
17-43801844-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-43801876-T-C		not specified	Uncertain significance (Oct 14, 2021)
17-43808994-G-A		not specified	Uncertain significance (Dec 20, 2021)
17-43809041-T-C		not specified	Uncertain significance (Nov 07, 2022)
17-43809062-C-T		not specified	Uncertain significance (Jun 03, 2024)
17-43810818-C-T		not specified	Uncertain significance (Jun 03, 2024)
17-43811158-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-43814023-C-T		not specified	Uncertain significance (Mar 21, 2024)
17-43814068-C-T		not specified	Uncertain significance (Mar 25, 2024)
17-43814212-G-C		not specified	Uncertain significance (May 23, 2023)
17-43814221-G-A		not specified	Uncertain significance (Jun 11, 2024)
17-43814241-T-C		not specified	Uncertain significance (Apr 17, 2023)
17-43818049-G-T		not specified	Uncertain significance (Nov 22, 2022)
17-43818067-G-T		not specified	Uncertain significance (May 08, 2023)
17-43818081-G-T		not specified	Uncertain significance (Jan 04, 2024)
17-43818087-G-A		not specified	Uncertain significance (May 02, 2024)
17-43818097-G-A		not specified	Uncertain significance (May 08, 2024)
17-43820968-C-T		not specified	Uncertain significance (Oct 12, 2022)
17-43820976-C-T		not specified	Uncertain significance (Aug 17, 2022)
17-43820977-G-A		not specified	Uncertain significance (May 28, 2024)
17-43823944-A-G		not specified	Uncertain significance (Sep 21, 2021)
17-43825775-T-A		not specified	Uncertain significance (Jun 07, 2024)
17-43827758-G-C		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPP3	protein_coding	protein_coding	ENST00000398389	18	32372

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000345	1.00	124754	0	62	124816	0.000248

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	261	352	0.742	0.0000215	3784
Missense in Polyphen		111	163.64	0.6783		1690
Synonymous	0.898	131	145	0.905	0.00000960	1128
Loss of Function	3.36	16	38.5	0.416	0.00000240	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00112
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000111
Finnish	0.0000498	0.0000464
European (Non-Finnish)	0.000160	0.000159
Middle Eastern	0.000112	0.000111
South Asian	0.000204	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.755
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.11

Haploinsufficiency Scores

• pHI: 0.855
• hipred: Y
• hipred_score: 0.685
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.624

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpp3
• Phenotype: vision/eye 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); cellular phenotype