MPZL3

protein-coding

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

Gene summary

Predicted to be involved in cell adhesion. Predicted to act upstream of or within extracellular matrix organization and hair cycle. Predicted to be located in membrane. Predicted to be active in plasma membrane. Implicated in lung cancer. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_198275.3

Inheritance

—

ClinVar variants

U:45B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.64

Max pathogenic AF

—

Genomic locus

chr11:118,226,690-118,252,365

External References & Databases

Ensembl (ENSG00000160588)

Transcript & Mutation Effects

hg38 • Region Span ~25.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MPZL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198275.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			42 clinvar	1 clinvar	2 clinvar	45
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	45	1	3	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198275.3	RefSeq	NP_938016.1	6	MANE Select
ENST00000278949.9	Ensembl	ENSP00000278949.4	6	MANE Select
NM_001286152.2	RefSeq	NP_001273081.1	6	Standard
ENST00000446386.2	Ensembl	ENSP00000393594.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion
extracellular matrix organization
hair cycle

Molecular Function

protein binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000278949
Coding exons: 6
Length: 25657
Individuals with no LoFs: 125654
Homozygous LoFs: 0
Heterozygous LoFs: 92
Defined: 125746
p: 0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.309	144	134	1.08	0.00000696	1515
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00066	0.00065	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00041	0.00040	rare
South Asian	0.00017	0.00016	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.246

Gene Damage Prediction

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