MLXIP

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

Basic information

Region (hg38): 12:122078755-122147344

Links

ENSG00000175727 ∙ NCBI:22877 ∙ OMIM:608090 ∙ HGNC:17055 ∙ Uniprot:Q9HAP2 ∙ 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 MLXIP gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MLXIP 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			11			11
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	0	0

Variants in MLXIP

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

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

Position	Type	Phenotype	Significance	ClinVar
12-122078959-G-T		not specified	Uncertain significance (Dec 16, 2021)
12-122078987-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-122078989-G-A		not specified	Uncertain significance (Dec 17, 2021)
12-122079031-C-T		not specified	Uncertain significance (Sep 26, 2023)
12-122079089-G-A		not specified	Uncertain significance (Jul 25, 2023)
12-122127883-A-G		not specified	Uncertain significance (Aug 29, 2022)
12-122129609-G-C		not specified	Uncertain significance (Dec 13, 2022)
12-122130061-T-C		not specified	Uncertain significance (Mar 23, 2023)
12-122133570-C-T		not specified	Uncertain significance (Dec 07, 2021)
12-122133717-G-A		not specified	Uncertain significance (Dec 19, 2022)
12-122133837-G-A		not specified	Uncertain significance (Nov 17, 2022)
12-122133969-A-G		not specified	Uncertain significance (Sep 26, 2023)
12-122135492-C-T		not specified	Uncertain significance (Oct 02, 2023)
12-122135586-G-A		not specified	Uncertain significance (Nov 14, 2023)
12-122138270-G-A		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MLXIP	protein_coding	protein_coding	ENST00000319080	17	115267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0107	124654	0	6	124660	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.25	377	521	0.723	0.0000318	5922
Missense in Polyphen		88	181.91	0.48375		2220
Synonymous	-0.492	236	227	1.04	0.0000152	1873
Loss of Function	4.76	5	35.7	0.140	0.00000153	427

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds DNA as a heterodimer with MLX and activates transcription. Binds to the canonical E box sequence 5'-CACGTG-3'. Plays a role in transcriptional activation of glycolytic target genes. Involved in glucose-responsive gene regulation. {ECO:0000250|UniProtKB:Q2VPU4, ECO:0000269|PubMed:12446771, ECO:0000269|PubMed:16782875}.
• Pathway: Insulin resistance - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.111

Haploinsufficiency Scores

• pHI: 0.166
• hipred: Y
• hipred_score: 0.728
• ghis: 0.570

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.698

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mlxip

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter
• Cellular component: nucleus;mitochondrial outer membrane
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein dimerization activity