MPZL1

myelin protein zero like 1, the group of V-set domain containing

Basic information

Region (hg38): 1:167721192-167791919

Links

ENSG00000197965

∙ NCBI:9019 ∙ OMIM:604376 ∙ HGNC:7226 ∙ Uniprot:O95297 ∙ 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 MPZL1 gene.

not_specified (28 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPZL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003953.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	2 clinvar	3
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	1	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPZL1	protein_coding	protein_coding	ENST00000359523	6	70728

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.159	0.827	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	101	136	0.744	0.00000722	1726
Missense in Polyphen		32	47.016	0.68062		603
Synonymous	0.424	51	55.0	0.927	0.00000316	554
Loss of Function	2.12	3	10.4	0.289	4.38e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.0000550	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Cell surface receptor, which is involved in signal transduction processes. Recruits PTPN11/SHP-2 to the cell membrane and is a putative substrate of PTPN11/SHP-2. Is a major receptor for concanavalin-A (ConA) and is involved in cellular signaling induced by ConA, which probably includes Src family tyrosine- protein kinases. Isoform 3 seems to have a dominant negative role; it blocks tyrosine phosphorylation of MPZL1 induced by ConA. Isoform 1, but not isoform 2 and isoform 3, may be involved in regulation of integrin-mediated cell motility. {ECO:0000269|PubMed:11751924, ECO:0000269|PubMed:12410637}.;
Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;TCR;EGFR1 (Consensus)

Intolerance Scores

loftool: 0.329
rvis_EVS: -0.32
rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

pHI: 0.0891
hipred: Y
hipred_score: 0.661
ghis: 0.587

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.924

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mpzl1
Phenotype: hematopoietic system phenotype; normal phenotype; immune system phenotype;

Gene ontology

Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;cell-cell signaling
Cellular component: integral component of plasma membrane;focal adhesion;cell surface
Molecular function: structural molecule activity;protein binding