DYDC1

DPY30 domain containing 1

Basic information

Region (hg38): 10:80336105-80356755

Links

ENSG00000170788 ∙ NCBI:143241 ∙ OMIM:615154 ∙ HGNC:23460 ∙ Uniprot:Q8WWB3 ∙ 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 DYDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYDC1 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			6	2		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	0

Variants in DYDC1

This is a list of pathogenic ClinVar variants found in the DYDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-80338513-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-80338530-G-T		not specified	Uncertain significance (Jun 21, 2023)
10-80339129-G-C		not specified	Uncertain significance (Dec 20, 2023)
10-80339129-G-T		not specified	Likely benign (Apr 11, 2023)
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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYDC1	protein_coding	protein_coding	ENST00000372204	6	20651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000260	0.790	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.208	81	86.4	0.937	0.00000420	1157
Missense in Polyphen		24	29.759	0.80648		374
Synonymous	0.714	24	28.9	0.831	0.00000139	300
Loss of Function	1.11	7	11.0	0.638	4.62e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000281	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.00147	0.00147
Finnish	0.00	0.00
European (Non-Finnish)	0.000111	0.000105
Middle Eastern	0.00147	0.00147
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a crucial role during acrosome biogenesis. {ECO:0000269|PubMed:19545932}.

Recessive Scores

• pRec: 0.0734

Intolerance Scores

• loftool: 0.526
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0845

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dydc1

Gene ontology

• Biological process: histone H3-K4 methylation
• Cellular component: Set1C/COMPASS complex
• Molecular function: protein binding