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.

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.

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					2	2
missense			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	2

Variants in MPZL1

This is a list of pathogenic ClinVar variants found in the MPZL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-167722165-C-A		not specified	Uncertain significance (Dec 27, 2023)
1-167722239-C-T		not specified	Uncertain significance (Oct 20, 2023)
1-167765608-A-C		not specified	Uncertain significance (May 26, 2023)
1-167765627-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-167765685-C-T		not specified	Uncertain significance (Oct 06, 2022)
1-167765686-G-A			Benign (May 09, 2018)
1-167765707-C-T			Benign (Jul 02, 2018)
1-167773263-T-C		not specified	Uncertain significance (Dec 13, 2023)
1-167773302-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-167773314-G-A		not specified	Uncertain significance (May 11, 2022)
1-167773355-C-T		not specified	Uncertain significance (Jun 02, 2024)
1-167776122-G-A		not specified	Uncertain significance (May 21, 2024)
1-167787822-C-G		not specified	Likely benign (May 31, 2023)
1-167787823-C-T		not specified	Uncertain significance (Oct 22, 2021)
1-167787865-A-G		not specified	Uncertain significance (Jan 06, 2023)
1-167787887-A-T		not specified	Uncertain significance (Feb 13, 2024)

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