DMC1

DNA meiotic recombinase 1

Basic information

Region (hg38): 22:38518948-38570204

Links

ENSG00000100206 ∙ NCBI:11144 ∙ OMIM:602721 ∙ HGNC:2927 ∙ Uniprot:Q14565 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DMC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DMC1 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			11		1	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	11	0	1

Variants in DMC1

This is a list of pathogenic ClinVar variants found in the DMC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-38521701-G-T		Azoospermia	Pathogenic (Dec 20, 2021)
22-38521710-G-A		not specified	Uncertain significance (Jul 25, 2023)
22-38538323-C-T		not specified	Uncertain significance (Aug 23, 2021)
22-38538340-G-T		not specified	Uncertain significance (Sep 17, 2021)
22-38538363-C-A		not specified	Uncertain significance (Dec 19, 2023)
22-38538391-C-T		not specified	Uncertain significance (Feb 05, 2024)
22-38538601-T-C		Premature ovarian failure	Benign (-)
22-38539368-T-C		not specified	Uncertain significance (Jul 08, 2022)
22-38539380-C-T		not specified	Uncertain significance (Nov 30, 2022)
22-38555372-T-C		Azoospermia	Pathogenic (Dec 20, 2021)
22-38562312-T-C		not specified	Uncertain significance (Dec 19, 2023)
22-38566611-T-A		not specified	Uncertain significance (Feb 05, 2024)
22-38566625-C-T		not specified	Uncertain significance (Nov 08, 2022)
22-38566702-C-T		not specified	Uncertain significance (Oct 16, 2024)
22-38566727-C-T			Uncertain significance (Jan 10, 2019)
22-38567623-G-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DMC1	protein_coding	protein_coding	ENST00000216024	13	51338

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000506	0.994	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	145	195	0.744	0.0000107	2235
Missense in Polyphen		50	80.142	0.62389		872
Synonymous	-0.301	67	63.9	1.05	0.00000352	639
Loss of Function	2.41	11	23.6	0.466	0.00000135	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000653	0.000653
South Asian	0.000229	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in meiotic recombination, specifically in homologous strand assimilation, which is required for the resolution of meiotic double-strand breaks. {ECO:0000250}.
• Pathway: Ovarian Infertility Genes (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.588
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.536
• hipred: Y
• hipred_score: 0.809
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.672

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dmc1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: DNA recombinase assembly;ovarian follicle development;oocyte maturation;mitotic recombination;synapsis;reciprocal meiotic recombination;male meiosis I;spermatogenesis;spermatid development;female gamete generation;strand invasion;meiotic cell cycle
• Cellular component: chromosome, telomeric region;condensed nuclear chromosome;nucleus;chromosome
• Molecular function: recombinase activity;DNA binding;double-stranded DNA binding;single-stranded DNA binding;protein binding;ATP binding;DNA-dependent ATPase activity