MCMDC2

minichromosome maintenance domain containing 2, the group of MCM family

Basic information

Region (hg38): 8:66870749-66922048

Previous symbols: [ "C8orf45" ]

Links

ENSG00000178460 ∙ NCBI:157777 ∙ OMIM:617545 ∙ HGNC:26368 ∙ Uniprot:Q4G0Z9 ∙ 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 MCMDC2 gene.

• not_specified (59 variants)
• not_provided (4 variants)
• Male_infertility_with_azoospermia_or_oligozoospermia_due_to_single_gene_mutation (2 variants)
• Azoospermia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCMDC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173518.5. 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
missense			57	2	2	61
nonsense	1	2				3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	2	57	2	3

Highest pathogenic variant AF is 0.00018465654

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCMDC2	protein_coding	protein_coding	ENST00000422365	14	51300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.24e-9	0.944	125555	0	187	125742	0.000744

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	269	323	0.833	0.0000151	4422
Missense in Polyphen		79	98.935	0.7985		1319
Synonymous	0.935	103	116	0.890	0.00000535	1309
Loss of Function	1.97	18	29.5	0.610	0.00000137	430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000668	0.000605
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.00	0.00
Finnish	0.00288	0.00287
European (Non-Finnish)	0.000781	0.000739
Middle Eastern	0.00	0.00
South Asian	0.000144	0.000131
Other	0.000996	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in meiotic recombination and associated DNA double-strand break repair. {ECO:0000250|UniProtKB:E9Q956}.

Intolerance Scores

• rvis_EVS: 1.16
• rvis_percentile_EVS: 92.59

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.197

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mcmdc2
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: DNA replication initiation;synaptonemal complex assembly;spermatogenesis;late meiotic recombination nodule assembly;oogenesis;double-strand break repair involved in meiotic recombination
• Molecular function: DNA binding;ATP binding