CSDC2

cold shock domain containing C2

Basic information

Region (hg38): 22:41561010-41577741

Links

ENSG00000172346 ∙ NCBI:27254 ∙ OMIM:617689 ∙ HGNC:30359 ∙ Uniprot:Q9Y534 ∙ 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 CSDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSDC2 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	1	0

Variants in CSDC2

This is a list of pathogenic ClinVar variants found in the CSDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-41571982-C-T		not specified	Uncertain significance (Jan 19, 2022)
22-41572003-C-T		not specified	Uncertain significance (May 07, 2024)
22-41572053-G-A		not specified	Uncertain significance (Aug 02, 2021)
22-41572064-G-C		not specified	Uncertain significance (Mar 23, 2022)
22-41572080-G-A		not specified	Likely benign (Oct 25, 2022)
22-41572092-C-T		not specified	Uncertain significance (Apr 12, 2022)
22-41572093-G-A		not specified	Uncertain significance (Jul 02, 2024)
22-41572113-C-G		not specified	Uncertain significance (Oct 29, 2024)
22-41572119-A-G		not specified	Uncertain significance (Jan 20, 2025)
22-41572129-G-C		not specified	Uncertain significance (Dec 01, 2022)
22-41573722-C-T		not specified	Uncertain significance (Oct 10, 2023)
22-41573774-C-T		not specified	Uncertain significance (Jun 21, 2023)
22-41574765-A-G		not specified	Uncertain significance (Jun 22, 2023)
22-41574779-A-C		not specified	Uncertain significance (Feb 07, 2025)
22-41577353-C-T		not specified	Uncertain significance (Aug 02, 2023)
22-41577355-C-T		not specified	Uncertain significance (Sep 02, 2024)
22-41577368-C-G		not specified	Uncertain significance (Sep 18, 2024)
22-41577431-C-T		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSDC2	protein_coding	protein_coding	ENST00000306149	3	16979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00312	0.613	125688	0	5	125693	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.790	61	81.0	0.753	0.00000526	956
Missense in Polyphen		23	34.231	0.6719		368
Synonymous	-0.972	45	37.4	1.20	0.00000280	323
Loss of Function	0.441	4	5.07	0.789	2.52e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000550	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding factor which binds specifically to the very 3'-UTR ends of both histone H1 and H3.3 mRNAs, encompassing the polyadenylation signal. Might play a central role in the negative regulation of histone variant synthesis in the developing brain (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.278
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.265
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.838

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csdc2

Gene ontology

• Biological process: regulation of transcription, DNA-templated;mRNA processing;regulation of mRNA stability
• Cellular component: nucleus;cytoplasm
• Molecular function: DNA binding;RNA binding;mRNA 3'-UTR binding;protein binding;transcription factor binding