MXD1

MAX dimerization protein 1, the group of MAX dimerization proteins|Basic helix-loop-helix proteins

Basic information

Region (hg38): 2:69897688-69942945

Previous symbols: [ "MAD" ]

Links

ENSG00000059728 ∙ NCBI:4084 ∙ OMIM:600021 ∙ HGNC:6761 ∙ Uniprot:Q05195 ∙ 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 MXD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MXD1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in MXD1

This is a list of pathogenic ClinVar variants found in the MXD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-69903190-G-A		not specified	Uncertain significance (Jul 31, 2024)
2-69916169-G-A		not specified	Uncertain significance (Oct 12, 2021)
2-69916193-A-G		not specified	Uncertain significance (Jul 07, 2024)
2-69935388-G-C		not specified	Uncertain significance (Feb 22, 2023)
2-69937296-G-A		not specified	Uncertain significance (Mar 27, 2023)
2-69937313-C-A		not specified	Uncertain significance (Mar 31, 2024)
2-69937364-G-A		not specified	Uncertain significance (Jun 27, 2022)
2-69937377-G-A		not specified	Uncertain significance (Jan 17, 2024)
2-69938105-G-A		not specified	Uncertain significance (Oct 01, 2024)
2-69938162-A-G		not specified	Uncertain significance (Jun 27, 2022)
2-69938204-G-A		not specified	Uncertain significance (Jul 25, 2023)
2-69938229-C-T		not specified	Uncertain significance (May 31, 2023)
2-69938248-G-T		not specified	Uncertain significance (Dec 06, 2022)
2-69938257-C-G		not specified	Uncertain significance (Apr 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MXD1	protein_coding	protein_coding	ENST00000264444	6	45258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.232	0.762	125726	0	2	125728	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	91	130	0.700	0.00000811	1465
Missense in Polyphen		25	49.619	0.50384		521
Synonymous	0.328	50	53.0	0.943	0.00000368	402
Loss of Function	2.34	3	11.6	0.259	7.24e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. MAD binds with MAX to form a sequence-specific DNA-binding protein complex which recognizes the core sequence 5'-CAC[GA]TG-3'. MAD thus antagonizes MYC transcriptional activity by competing for MAX.
• Pathway: Vitamin D Receptor Pathway;Preimplantation Embryo;overview of telomerase protein component gene htert transcriptional regulation;Regulation of Telomerase;Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.230
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.938
• hipred: Y
• hipred_score: 0.743
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mxd1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;multicellular organism development;cell population proliferation
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;mitochondrion;cytosol
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coregulator activity;transcription corepressor activity;protein binding;protein dimerization activity