MLXIPL

MLX interacting protein like, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 7:73593193-73624543

Previous symbols: [ "WBSCR14" ]

Links

ENSG00000009950 ∙ NCBI:51085 ∙ OMIM:605678 ∙ HGNC:12744 ∙ Uniprot:Q9NP71 ∙ 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 MLXIPL gene.

• not provided (49 variants)
• Inborn genetic diseases (32 variants)
• Williams syndrome (2 variants)
• not specified (1 variants)
• MLXIPL-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MLXIPL 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	8	23
missense			32	9	8	49
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				5	3	8
non coding					2	2
Total	0	0	33	24	18

Variants in MLXIPL

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

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

Position	Type	Phenotype	Significance	ClinVar
7-73593276-T-C			Benign (Aug 23, 2019)
7-73593903-G-A			Likely benign (Apr 01, 2024)
7-73593923-C-A		not specified	Uncertain significance (Apr 13, 2023)
7-73593934-G-A			Benign (Dec 31, 2019)
7-73594286-C-T			Likely benign (Oct 23, 2018)
7-73594330-C-T		not specified	Uncertain significance (Jul 21, 2021)
7-73595675-C-T			Benign (Jul 11, 2017)
7-73595695-C-T		not specified	Uncertain significance (May 23, 2023)
7-73595847-G-A			Likely benign (Jul 31, 2018)
7-73595861-C-T			Likely benign (Dec 31, 2019)
7-73595904-C-T			Benign (Dec 31, 2019)
7-73595977-C-T			Likely benign (May 30, 2018)
7-73596166-T-G		not specified	Uncertain significance (Feb 28, 2024)
7-73596240-C-T			Likely benign (Dec 31, 2019)
7-73596243-G-A			Likely benign (Jun 29, 2018)
7-73596259-C-T		not specified	Uncertain significance (Apr 08, 2022)
7-73596365-T-G		not specified	Uncertain significance (Apr 18, 2023)
7-73596403-C-T			Likely benign (Aug 08, 2018)
7-73596417-G-A		not specified	Uncertain significance (Dec 21, 2022)
7-73596471-G-A		not specified	Uncertain significance (Aug 12, 2021)
7-73596640-G-A			Likely benign (Mar 01, 2023)
7-73596648-C-A			Likely benign (Jul 02, 2018)
7-73596650-G-C		not specified	Uncertain significance (Oct 22, 2021)
7-73596653-G-C		not specified	Uncertain significance (Feb 28, 2023)
7-73596664-C-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MLXIPL	protein_coding	protein_coding	ENST00000313375	17	31350

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0478	0.952	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	391	466	0.839	0.0000298	5359
Missense in Polyphen		162	190.92	0.84853		2234
Synonymous	0.891	179	195	0.919	0.0000121	1804
Loss of Function	3.90	9	33.2	0.271	0.00000161	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000139	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000102	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000661	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Binds to the canonical and non-canonical E box sequences 5'-CACGTG-3' (By similarity). {ECO:0000250}.
• Disease: DISEASE: Note=WBSCR14 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of WBSCR14 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease. {ECO:0000269|PubMed:10780788}.
• Pathway: Insulin resistance - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Metformin Pathway, Pharmacodynamic;Angiopoietin Like Protein 8 Regulatory Pathway;Liver steatosis AOP;chrebp regulation by carbohydrates and camp;PKA-mediated phosphorylation of key metabolic factors;AMPK inhibits chREBP transcriptional activation activity;PP2A-mediated dephosphorylation of key metabolic factors;Metabolism;ChREBP activates metabolic gene expression;Integration of energy metabolism (Consensus)

Intolerance Scores

• loftool: 0.427
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.87

Haploinsufficiency Scores

• pHI: 0.737
• hipred: Y
• hipred_score: 0.703
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mlxipl
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; liver/biliary system phenotype; 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;positive regulation of cell population proliferation;anatomical structure morphogenesis;glucose mediated signaling pathway;negative regulation of peptidyl-serine phosphorylation;intracellular signal transduction;glucose homeostasis;positive regulation of fatty acid biosynthetic process;positive regulation of glycolytic process;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of lipid biosynthetic process;fatty acid homeostasis;triglyceride homeostasis;negative regulation of cell cycle arrest;negative regulation of oxidative phosphorylation;energy homeostasis
• Cellular component: nucleus;nucleoplasm;transcription factor complex;cytoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription factor binding;carbohydrate response element binding;protein homodimerization activity;protein heterodimerization activity