MLIP

muscular LMNA interacting protein

Basic information

Region (hg38): 6:53929981-54266280

Previous symbols: [ "C6orf142" ]

Links

ENSG00000146147 ∙ NCBI:90523 ∙ OMIM:614106 ∙ HGNC:21355 ∙ Uniprot:Q5VWP3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis (Strong), mode of inheritance: AR
• myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis	AR	Cardiovascular; Musculoskeletal	The condition can involve cardiomyopathy and/or arrhythmia, and awareness may allow prompt diagnosis and mangement; Individuals may be at risk of rhabdomyolysis, and awareness may allow avoidance of precipitating factors, and prompt treatment of episodes	Cardiovascular; Musculoskeletal	34581780; 34935254; 35672413; 35915960

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MLIP 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						0
missense			22	1	3	26
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	0	2	22	1	3

Variants in MLIP

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

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

Position	Type	Phenotype	Significance	ClinVar
6-54019068-A-G		Inborn genetic diseases	Likely benign (Aug 28, 2021)
6-54124549-C-T		Inborn genetic diseases	Uncertain significance (Jul 05, 2023)
6-54124564-C-T		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
6-54124577-A-C		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
6-54124591-C-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
6-54124611-C-A		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
6-54124648-T-C		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
6-54124708-G-C		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
6-54124758-A-T		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)
6-54124780-G-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
6-54124840-T-C		Inborn genetic diseases	Uncertain significance (May 11, 2022)
6-54124848-C-T		Myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis	Pathogenic (Nov 29, 2022)
6-54124860-G-T		Inborn genetic diseases	Uncertain significance (Dec 16, 2023)
6-54124861-G-A		Inborn genetic diseases	Uncertain significance (Apr 17, 2023)
6-54137630-A-G			Uncertain significance (Jun 08, 2023)
6-54137807-CA-C		Myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis	Pathogenic (Nov 29, 2022)
6-54137812-G-A			Likely benign (Jul 01, 2024)
6-54137894-A-T		Myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis	Pathogenic (Nov 29, 2022)
6-54137898-GT-G		Myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis	Pathogenic (Nov 29, 2022)
6-54149059-T-A		Inborn genetic diseases	Uncertain significance (May 23, 2023)
6-54149075-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Apr 01, 2023)
6-54149109-AT-A		Myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis	Pathogenic (Nov 29, 2022)
6-54149122-C-T		Myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis	Pathogenic (Nov 29, 2022)
6-54160375-T-A		Inborn genetic diseases	Uncertain significance (Oct 14, 2021)
6-54160386-A-G		Inborn genetic diseases	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MLIP	protein_coding	protein_coding	ENST00000274897	13	336299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.16e-16	0.00985	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.710	266	235	1.13	0.0000114	2964
Missense in Polyphen		84	88.341	0.95086		1145
Synonymous	-0.613	97	89.6	1.08	0.00000462	895
Loss of Function	0.0556	24	24.3	0.988	0.00000108	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000608	0.000597
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000161	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.000329	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for precocious cardiac adaptation to stress through integrated regulation of the AKT/mTOR pathways and FOXO1. Regulates cardiac homeostasis and plays an important role in protection against cardiac hypertrophy. Acts as a transcriptional cofactor, represses transactivator activity of ISL1 and MYOCD. {ECO:0000250|UniProtKB:A0A096MK47, ECO:0000250|UniProtKB:Q5FW52}.

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.51

Haploinsufficiency Scores

• pHI: 0.728
• hipred: N
• hipred_score: 0.123
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mlip
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of cardiac muscle hypertrophy;positive regulation of transcription by RNA polymerase II;negative regulation of cardiac muscle hypertrophy in response to stress
• Cellular component: nucleus;nuclear envelope;PML body;nuclear lumen;sarcolemma