DMRTC2

DMRT like family C2

Basic information

Region (hg38): 19:41844743-41852333

Links

ENSG00000142025 ∙ NCBI:63946 ∙ OMIM:614806 ∙ HGNC:13911 ∙ Uniprot:Q8IXT2 ∙ 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 DMRTC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DMRTC2 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in DMRTC2

This is a list of pathogenic ClinVar variants found in the DMRTC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41847460-A-G		not specified	Uncertain significance (Nov 03, 2022)
19-41847480-C-T		not specified	Uncertain significance (Jun 04, 2024)
19-41847532-C-T		not specified	Uncertain significance (Dec 13, 2022)
19-41847565-G-A		not specified	Uncertain significance (Apr 08, 2024)
19-41847603-C-T		not specified	Uncertain significance (Mar 08, 2024)
19-41847773-C-T		not specified	Uncertain significance (Mar 31, 2023)
19-41847793-G-C		not specified	Uncertain significance (May 31, 2023)
19-41848523-G-A		not specified	Uncertain significance (Oct 10, 2023)
19-41848951-G-A		not specified	Uncertain significance (May 02, 2024)
19-41848969-T-G		not specified	Uncertain significance (May 28, 2024)
19-41850346-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-41850550-C-T		not specified	Likely benign (Dec 27, 2023)
19-41850604-G-A		not specified	Uncertain significance (May 08, 2024)
19-41850617-A-T		not specified	Uncertain significance (Nov 22, 2022)
19-41850628-G-T		not specified	Uncertain significance (Jul 13, 2021)
19-41850647-C-A		not specified	Uncertain significance (Feb 28, 2024)
19-41850695-C-T		not specified	Uncertain significance (Jul 12, 2023)
19-41851613-G-C		not specified	Uncertain significance (Jan 30, 2024)
19-41851641-C-T		not specified	Uncertain significance (Mar 13, 2023)
19-41851659-A-G		not specified	Uncertain significance (Feb 23, 2023)
19-41851667-C-T		not specified	Uncertain significance (Jul 14, 2023)
19-41851675-G-A			Likely benign (Apr 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DMRTC2	protein_coding	protein_coding	ENST00000269945	8	7596

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.731	0.269	125701	0	42	125743	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.914	175	212	0.824	0.0000120	2304
Missense in Polyphen		45	68.598	0.656		726
Synonymous	-0.750	91	82.3	1.11	0.00000446	815
Loss of Function	3.21	3	17.5	0.172	8.90e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000126
Ashkenazi Jewish	0.000992	0.000993
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in sexual development. {ECO:0000269|PubMed:11863363}.

Recessive Scores

• pRec: 0.0851

Intolerance Scores

• loftool: 0.210
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.399
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.239

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dmrtc2
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;male meiosis I;spermatid nucleus elongation;sex differentiation;biological_process;positive regulation of histone H3-K9 dimethylation;positive regulation of histone H3-K9 trimethylation
• Cellular component: XY body;cellular_component;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;protein homodimerization activity;sequence-specific DNA binding;metal ion binding