DYDC2

DPY30 domain containing 2

Basic information

Region (hg38): 10:80344745-80368073

Links

ENSG00000133665 ∙ NCBI:84332 ∙ ∙ HGNC:23468 ∙ Uniprot:Q96IM9 ∙ 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 DYDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYDC2 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			7	2	1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding			3	1		4
Total	0	0	10	3	2

Variants in DYDC2

This is a list of pathogenic ClinVar variants found in the DYDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-80351975-G-A		not specified	Uncertain significance (Nov 18, 2022)
10-80351984-T-C		not specified	Likely benign (May 31, 2022)
10-80352456-A-C		not specified	Uncertain significance (Oct 29, 2024)
10-80352469-T-C		not specified	Uncertain significance (Aug 11, 2024)
10-80352523-C-T		not specified	Uncertain significance (Dec 22, 2023)
10-80352528-C-T		not specified	Uncertain significance (Apr 26, 2023)
10-80352573-A-G		not specified	Uncertain significance (Mar 25, 2024)
10-80362498-G-T		not specified	Uncertain significance (Feb 02, 2022)
10-80362513-G-T			Benign (Oct 24, 2018)
10-80362516-C-T		not specified	Uncertain significance (Jun 28, 2024)
10-80362573-G-A		not specified	Uncertain significance (Jul 09, 2024)
10-80362586-A-T		not specified	Uncertain significance (Jun 21, 2021)
10-80362949-A-G			Benign (Dec 31, 2019)
10-80362952-A-G		not specified	Uncertain significance (Nov 14, 2024)
10-80362961-A-C		not specified	Uncertain significance (Sep 09, 2024)
10-80363006-T-C		not specified	Likely benign (Mar 01, 2024)
10-80363053-A-C		not specified	Uncertain significance (Jun 29, 2023)
10-80366718-A-G		not specified	Uncertain significance (Mar 01, 2024)
10-80366803-T-C		not specified	Uncertain significance (Nov 08, 2022)
10-80366811-A-G		not specified	Uncertain significance (Feb 27, 2024)
10-80366910-G-A		not specified	Likely benign (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYDC2	protein_coding	protein_coding	ENST00000372198	4	23329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00349	0.637	125165	4	575	125744	0.00231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.410	84	95.3	0.882	0.00000436	1272
Missense in Polyphen		11	20.292	0.54209		283
Synonymous	-0.0898	33	32.4	1.02	0.00000152	332
Loss of Function	0.511	4	5.27	0.760	2.21e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0312	0.0314
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000381	0.000381
South Asian	0.000165	0.000163
Other	0.000984	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0622

Intolerance Scores

• loftool: 0.800
• rvis_EVS: 0.88
• rvis_percentile_EVS: 88.96

Haploinsufficiency Scores

• pHI: 0.0472
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dydc2

Gene ontology

• Biological process: histone H3-K4 methylation
• Cellular component: Set1C/COMPASS complex