MXD4

MAX dimerization protein 4, the group of MAX dimerization proteins|MicroRNA protein coding host genes|Basic helix-loop-helix proteins

Basic information

Region (hg38): 4:2247432-2262109

Links

ENSG00000123933 ∙ NCBI:10608 ∙ OMIM:620016 ∙ HGNC:13906 ∙ Uniprot:Q14582 ∙ 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 MXD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MXD4 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in MXD4

This is a list of pathogenic ClinVar variants found in the MXD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-2250561-G-A		not specified	Uncertain significance (Mar 04, 2024)
4-2250597-C-T		not specified	Uncertain significance (Apr 07, 2023)
4-2250627-G-A		not specified	Uncertain significance (Jan 02, 2024)
4-2251104-G-A		not specified	Uncertain significance (Dec 01, 2022)
4-2251144-C-T		not specified	Uncertain significance (Aug 16, 2021)
4-2252445-G-A		not specified	Uncertain significance (Jan 09, 2024)
4-2261734-G-C		not specified	Uncertain significance (Oct 05, 2023)
4-2261752-C-A		not specified	Uncertain significance (Feb 23, 2023)
4-2261760-C-G		not specified	Uncertain significance (Jun 11, 2021)
4-2261777-C-A		not specified	Uncertain significance (Dec 03, 2021)
4-2261807-C-T		not specified	Uncertain significance (Jan 23, 2023)
4-2261969-G-C		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MXD4	protein_coding	protein_coding	ENST00000337190	6	14863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.776	0.222	125356	0	3	125359	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.737	97	120	0.810	0.00000810	1310
Missense in Polyphen		33	49.551	0.66598		546
Synonymous	-1.61	70	54.9	1.28	0.00000384	423
Loss of Function	2.52	1	9.30	0.107	4.93e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000103	0.0000925
European (Non-Finnish)	0.00000884	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Binds with MAX to form a sequence-specific DNA-binding protein complex which recognizes the core sequence 5'-CAC[GA]TG-3'. Antagonizes MYC transcriptional activity by competing for MAX and suppresses MYC dependent cell transformation (By similarity). {ECO:0000250}.
• Pathway: Validated targets of C-MYC transcriptional repression (Consensus)

Recessive Scores

• pRec: 0.0941

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.212
• hipred: Y
• hipred_score: 0.714
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mxd4

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of cell population proliferation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;transcription corepressor activity;protein binding;protein dimerization activity