MPZL2

myelin protein zero like 2, the group of V-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 11:118253416-118264536

Previous symbols: [ "EVA1" ]

Links

ENSG00000149573 ∙ NCBI:10205 ∙ OMIM:604873 ∙ HGNC:3496 ∙ Uniprot:O60487 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal recessive 111 (Strong), mode of inheritance: AR
• hearing loss, autosomal recessive 111 (Definitive), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• hearing loss, autosomal recessive 111 (Strong), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 111	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	29961571; 29982980

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MPZL2 gene.

• Hearing loss, autosomal recessive 111 (3 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPZL2 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				6	1	7
missense		1	12		1	14
nonsense	1	3				4
start loss		1				1
frameshift	2	4				6
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding				1	4	5
Total	4	9	12	7	6

Highest pathogenic variant AF is 0.000210

Variants in MPZL2

This is a list of pathogenic ClinVar variants found in the MPZL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118257248-T-G		MPZL2-related disorder	Likely benign (Apr 03, 2019)
11-118257268-A-G		MPZL2-related disorder	Likely benign (Nov 01, 2019)
11-118257295-G-A		MPZL2-related disorder	Likely benign (Sep 14, 2020)
11-118257298-C-G		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
11-118260093-C-T		Inborn genetic diseases • MPZL2-related disorder	Uncertain significance (Apr 25, 2022)
11-118260094-G-A		Hearing loss, autosomal recessive 111	Likely pathogenic (Dec 07, 2021)
11-118260126-A-G		Inborn genetic diseases	Uncertain significance (Aug 08, 2022)
11-118260165-A-G		Inborn genetic diseases	Uncertain significance (Oct 25, 2023)
11-118260174-GC-G		Hearing loss, autosomal recessive 111	Pathogenic (Dec 13, 2022)
11-118260186-A-G			Uncertain significance (Jun 20, 2024)
11-118260199-G-A		Inborn genetic diseases	Uncertain significance (Apr 19, 2023)
11-118260201-A-G		MPZL2-related disorder	Likely benign (Jun 11, 2024)
11-118260334-T-C			Benign (May 13, 2021)
11-118260427-A-G			Benign (May 26, 2021)
11-118262447-C-G		Inborn genetic diseases	Uncertain significance (Jun 08, 2022)
11-118262451-G-A		MPZL2-related disorder	Likely benign (Dec 16, 2019)
11-118262456-GC-G		Hearing loss, autosomal recessive 111	Likely pathogenic (Mar 29, 2024)
11-118262458-C-T		MPZL2-related disorder	Benign (Jun 06, 2019)
11-118262488-G-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Sep 04, 2024)
11-118262529-G-A		MPZL2-related disorder	Likely benign (Apr 29, 2019)
11-118262532-C-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
11-118262534-G-A			Likely pathogenic (Nov 11, 2021)
11-118262543-A-G		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
11-118262553-G-GGA		Hearing loss, autosomal recessive 111	Likely pathogenic (Jan 02, 2020)
11-118262566-C-T		Inborn genetic diseases	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPZL2	protein_coding	protein_coding	ENST00000278937	5	11134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-12	0.00627	125280	0	466	125746	0.00185

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.480	147	132	1.12	0.00000778	1397
Missense in Polyphen		55	42.578	1.2917		446
Synonymous	-0.290	49	46.5	1.05	0.00000253	431
Loss of Function	-1.08	16	12.0	1.34	6.94e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00294	0.00294
Ashkenazi Jewish	0.00378	0.00378
East Asian	0.00583	0.00583
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00167	0.00166
Middle Eastern	0.00583	0.00583
South Asian	0.000850	0.000850
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates homophilic cell-cell adhesion.
• Pathway: Differentiation of white and brown adipocyte (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.557
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.276
• hipred: N
• hipred_score: 0.195
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpzl2
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;anatomical structure morphogenesis
• Cellular component: cytoskeleton;integral component of membrane
• Molecular function: protein binding