MYLIP

myosin regulatory light chain interacting protein, the group of MicroRNA protein coding host genes|Ring finger proteins|FERM domain containing

Basic information

Region (hg38): 6:16129086-16151367

Links

ENSG00000007944 ∙ NCBI:29116 ∙ OMIM:610082 ∙ HGNC:21155 ∙ Uniprot:Q8WY64 ∙ 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 MYLIP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYLIP 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				15	3	18
missense			37	4	2	43
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			2			2
non coding			2	5		7
Total	0	0	41	24	5

Variants in MYLIP

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

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

Position	Type	Phenotype	Significance	ClinVar
6-16129372-T-C			Uncertain significance (Sep 20, 2021)
6-16129378-C-A		not specified	Uncertain significance (Sep 14, 2023)
6-16129411-T-C			Uncertain significance (Jan 23, 2023)
6-16130620-G-A			Likely benign (Dec 22, 2023)
6-16130665-A-T			Uncertain significance (Nov 22, 2023)
6-16130723-A-G		not specified	Uncertain significance (Apr 08, 2024)
6-16141654-C-A			Uncertain significance (Jan 31, 2023)
6-16141688-G-A			Likely benign (Jan 14, 2024)
6-16141707-G-T		not specified	Uncertain significance (Jun 21, 2021)
6-16141722-A-T			Uncertain significance (Nov 01, 2023)
6-16141726-A-T		not specified	Uncertain significance (Jun 05, 2023)
6-16141730-T-G		not specified	Uncertain significance (Jul 20, 2023)
6-16141819-G-A			Likely benign (Aug 19, 2022)
6-16143017-C-T			Uncertain significance (Feb 28, 2022)
6-16143021-A-G		not specified	Uncertain significance (Jul 13, 2022)
6-16143095-G-A			Likely benign (Aug 24, 2022)
6-16143097-C-T			Uncertain significance (Nov 18, 2023)
6-16143106-A-T		not specified	Uncertain significance (May 04, 2022)
6-16143118-A-G			Uncertain significance (May 11, 2022)
6-16143129-G-A		not specified	Uncertain significance (Aug 21, 2023)
6-16143132-C-T		not specified	Uncertain significance (Mar 27, 2024)
6-16143157-T-A		not specified	Uncertain significance (Apr 30, 2024)
6-16143159-A-C			Benign (Jan 25, 2024)
6-16143206-C-G			Likely benign (Dec 27, 2022)
6-16143721-A-G		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYLIP	protein_coding	protein_coding	ENST00000356840	7	19124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.184	0.815	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	205	253	0.809	0.0000138	2923
Missense in Polyphen		42	74.891	0.56081		859
Synonymous	0.0306	105	105	0.996	0.00000634	849
Loss of Function	3.06	5	19.6	0.255	9.17e-7	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of myosin regulatory light chain (MRLC), LDLR, VLDLR and LRP8. Activity depends on E2 enzymes of the UBE2D family. Proteasomal degradation of MRLC leads to inhibit neurite outgrowth in presence of NGF by counteracting the stabilization of MRLC by saposin-like protein (CNPY2/MSAP) and reducing CNPY2-stimulated neurite outgrowth. Acts as a sterol- dependent inhibitor of cellular cholesterol uptake by mediating ubiquitination and subsequent degradation of LDLR. {ECO:0000269|PubMed:10593918, ECO:0000269|PubMed:12826659, ECO:0000269|PubMed:14550572, ECO:0000269|PubMed:19520913, ECO:0000269|PubMed:20427281, ECO:0000269|PubMed:22109552}.
• Pathway: Cholesterol metabolism - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Immune System;VLDLR internalisation and degradation;Plasma lipoprotein clearance;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Transport of small molecules;Class I MHC mediated antigen processing & presentation;Plasma lipoprotein assembly, remodeling, and clearance (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.232
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.201
• hipred: Y
• hipred_score: 0.765
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mylip
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein polyubiquitination;ubiquitin-dependent protein catabolic process;nervous system development;negative regulation of neuron projection development;negative regulation of low-density lipoprotein particle clearance;protein ubiquitination;protein destabilization;low-density lipoprotein particle receptor catabolic process;regulation of low-density lipoprotein particle receptor catabolic process;cholesterol homeostasis;positive regulation of protein catabolic process
• Cellular component: cytosol;cytoskeleton;plasma membrane
• Molecular function: ubiquitin-protein transferase activity;protein binding;cytoskeletal protein binding;metal ion binding;ubiquitin protein ligase activity