MDM1

Mdm1 nuclear protein

Basic information

Region (hg38): 12:68272443-68332381

Links

ENSG00000111554 ∙ NCBI:56890 ∙ OMIM:613813 ∙ HGNC:29917 ∙ Uniprot:Q8TC05 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MDM1 gene.

• not_specified (97 variants)
• not_provided (3 variants)
• Neurodevelopmental_disorder (1 variants)
• Retinal_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MDM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001354969.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			92	6		98
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	7	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MDM1	protein_coding	protein_coding	ENST00000303145	14	59939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.72e-12	0.934	125669	0	79	125748	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.151	363	371	0.978	0.0000189	4642
Missense in Polyphen		145	140.22	1.0341		1792
Synonymous	0.463	124	131	0.949	0.00000675	1348
Loss of Function	2.08	24	37.8	0.634	0.00000201	473

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00145	0.00145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000230	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.000230	0.000217
South Asian	0.000510	0.000490
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-binding protein that negatively regulates centriole duplication. Binds to and stabilizes microtubules (PubMed:26337392). {ECO:0000269|PubMed:26337392}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.940
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.66

Haploinsufficiency Scores

• pHI: 0.423
• hipred: N
• hipred_score: 0.145
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mdm1
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); pigmentation phenotype

Gene ontology

• Biological process: photoreceptor cell maintenance;negative regulation of centriole replication;retina development in camera-type eye
• Cellular component: nucleus;centrosome;centriole;cytosol;microtubule
• Molecular function: microtubule binding