MXD3

MAX dimerization protein 3, the group of Basic helix-loop-helix proteins|MAX dimerization proteins

Basic information

Region (hg38): 5:177301461-177312757

Links

ENSG00000213347 ∙ NCBI:83463 ∙ OMIM:609450 ∙ HGNC:14008 ∙ Uniprot:Q9BW11 ∙ 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 MXD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MXD3 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				1		1
missense			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in MXD3

This is a list of pathogenic ClinVar variants found in the MXD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-177301801-T-C		not specified	Uncertain significance (Jan 23, 2024)
5-177301955-C-T		not specified	Uncertain significance (Sep 27, 2022)
5-177301986-G-C		not specified	Uncertain significance (Jul 14, 2024)
5-177302411-T-C		not specified	Uncertain significance (Nov 09, 2024)
5-177302445-G-C		not specified	Uncertain significance (Mar 01, 2023)
5-177302584-A-G		not specified	Uncertain significance (Dec 10, 2024)
5-177302603-C-G		not specified	Uncertain significance (Jun 11, 2024)
5-177304019-C-T		not specified	Uncertain significance (Apr 20, 2023)
5-177304031-G-T		not specified	Uncertain significance (Nov 03, 2023)
5-177304647-A-T		not specified	Uncertain significance (Feb 23, 2023)
5-177306140-A-G		not specified	Uncertain significance (Dec 27, 2023)
5-177306521-C-T		not specified	Uncertain significance (Mar 02, 2023)
5-177306541-A-C		not specified	Likely benign (Nov 13, 2024)
5-177306544-C-A		not specified	Uncertain significance (Jan 07, 2022)
5-177306561-G-T		not specified	Uncertain significance (Jun 27, 2023)
5-177306563-T-G		not specified	Uncertain significance (Jan 26, 2023)
5-177307602-C-T		not specified	Uncertain significance (Mar 28, 2024)
5-177307638-C-T		not specified	Uncertain significance (Jul 12, 2023)
5-177307697-A-G		not specified	Uncertain significance (Apr 25, 2023)
5-177307796-A-G		not specified	Uncertain significance (Feb 22, 2023)
5-177307810-A-G		not specified	Uncertain significance (Oct 20, 2021)
5-177307831-T-C		not specified	Uncertain significance (Aug 23, 2021)
5-177307853-C-T		not specified	Uncertain significance (Jun 05, 2023)
5-177307856-C-T		not specified	Uncertain significance (Dec 07, 2024)
5-177307873-C-G		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MXD3	protein_coding	protein_coding	ENST00000439742	6	11297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00310	0.831	125674	0	22	125696	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.194	120	126	0.951	0.00000896	1280
Missense in Polyphen		44	49.386	0.89094		522
Synonymous	-1.66	72	56.2	1.28	0.00000355	424
Loss of Function	1.15	5	8.64	0.579	3.66e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000159	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000901	0.0000880
Middle Eastern	0.000165	0.000163
South Asian	0.000197	0.000196
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}.

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.439
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mxd3
• Phenotype: cellular phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;protein dimerization activity