MPZL3

myelin protein zero like 3, the group of V-set domain containing

Basic information

Region (hg38): 11:118226690-118252365

Links

ENSG00000160588 ∙ NCBI:196264 ∙ OMIM:611707 ∙ HGNC:27279 ∙ Uniprot:Q6UWV2 ∙ 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 MPZL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPZL3 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			17		2	19
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	3

Variants in MPZL3

This is a list of pathogenic ClinVar variants found in the MPZL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118229905-C-T		not specified	Uncertain significance (Dec 26, 2023)
11-118233464-C-T		not specified	Uncertain significance (May 17, 2023)
11-118233486-G-T		not specified	Uncertain significance (Mar 17, 2023)
11-118233495-TAC-T			Benign (Dec 31, 2019)
11-118235430-G-A		not specified	Uncertain significance (Mar 06, 2023)
11-118235470-T-C		not specified	Uncertain significance (Aug 12, 2021)
11-118235491-T-G		not specified	Uncertain significance (Apr 08, 2022)
11-118235506-C-A		not specified	Uncertain significance (Sep 09, 2024)
11-118235524-C-T		not specified	Uncertain significance (Sep 11, 2024)
11-118235527-C-T			Benign (May 21, 2018)
11-118235550-A-G		not specified	Uncertain significance (Feb 15, 2023)
11-118235562-G-T		not specified	Uncertain significance (Jul 30, 2024)
11-118235578-T-C			Benign (Jun 18, 2018)
11-118237131-C-T		not specified	Uncertain significance (Oct 20, 2023)
11-118237164-T-C		not specified	Uncertain significance (Apr 29, 2024)
11-118237173-C-A		not specified	Uncertain significance (Jul 12, 2023)
11-118237196-C-G		not specified	Uncertain significance (May 24, 2023)
11-118240242-T-C		not specified	Uncertain significance (Mar 13, 2023)
11-118240258-T-C		not specified	Uncertain significance (May 09, 2023)
11-118240270-T-C		not specified	Uncertain significance (Oct 27, 2021)
11-118240317-C-G		not specified	Uncertain significance (Feb 15, 2023)
11-118240326-C-T		not specified	Uncertain significance (Apr 09, 2024)
11-118252264-C-G		not specified	Uncertain significance (Jul 30, 2023)
11-118252276-C-A		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPZL3	protein_coding	protein_coding	ENST00000278949	6	25657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.24e-14	0.00124	125654	0	92	125746	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.309	144	134	1.08	0.00000696	1515
Missense in Polyphen		50	43.211	1.1571		521
Synonymous	-0.299	53	50.3	1.05	0.00000265	474
Loss of Function	-1.91	17	10.4	1.64	5.23e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000858	0.000857
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000657	0.000653
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000405	0.000404
Middle Eastern	0.000657	0.000653
South Asian	0.000171	0.000163
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates homophilic cell-cell adhesion. {ECO:0000250}.

Recessive Scores

• pRec: 0.0933

Intolerance Scores

• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.178
• hipred: N
• hipred_score: 0.144
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.246

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpzl3
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; skeleton phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; pigmentation phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;extracellular matrix organization;hair cycle
• Cellular component: integral component of membrane
• Molecular function: protein binding