MCM6

minichromosome maintenance complex component 6, the group of MCM family|minichromosome maintenance 2-7 complex

Basic information

Region (hg38): 2:135839626-135876443

Links

ENSG00000076003

∙ NCBI:4175 ∙ OMIM:601806 ∙ HGNC:6949 ∙ Uniprot:Q14566 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lactose intolerance, adult type; Lactase persistence	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Gastrointestinal	7543318; 9481112; 11788828; 12915462; 15114531; 16041375; 15928901; 16019716; 17120047; 17159977; 18179885

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MCM6 gene.

not_specified (89 variants)
MCM6-related_disorder (13 variants)
not_provided (10 variants)
Nonpersistence_of_intestinal_lactase (6 variants)
LACTASE_PERSISTENCE (5 variants)
Neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCM6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005915.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	2 clinvar	7
missense			93 clinvar	5 clinvar	1 clinvar	99
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	95	10	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCM6	protein_coding	protein_coding	ENST00000264156	17	36801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.978	0.0217	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	390	454	0.859	0.0000245	5387
Missense in Polyphen		111	171.04	0.64898		1991
Synonymous	0.764	147	159	0.923	0.00000817	1572
Loss of Function	5.05	7	42.6	0.164	0.00000247	504

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. {ECO:0000269|PubMed:9305914}.;
Pathway: Cell cycle - Homo sapiens (human);DNA replication - Homo sapiens (human);Cell Cycle;Retinoblastoma (RB) in Cancer;G1 to S cell cycle control;DNA Replication;cdk regulation of dna replication;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Activation of the pre-replicative complex;Unwinding of DNA;Mitotic G1-G1/S phases;Orc1 removal from chromatin;DNA Replication;Switching of origins to a post-replicative state;DNA strand elongation;Synthesis of DNA;S Phase;G1/S Transition;Assembly of the pre-replicative complex;DNA Replication Pre-Initiation;M/G1 Transition;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

pRec: 0.206

Intolerance Scores

loftool: 0.480
rvis_EVS: -0.57
rvis_percentile_EVS: 18.9

Haploinsufficiency Scores

pHI: 0.981
hipred: Y
hipred_score: 0.831
ghis: 0.697

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.546

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mcm6
Phenotype: cellular phenotype; growth/size/body region phenotype; neoplasm; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: G1/S transition of mitotic cell cycle;DNA replication;DNA unwinding involved in DNA replication;DNA replication initiation
Cellular component: nuclear chromosome, telomeric region;nucleus;nucleoplasm;MCM complex
Molecular function: single-stranded DNA binding;ATP-dependent DNA helicase activity;protein binding;ATP binding;identical protein binding