CSDC2

cold shock domain containing C2

Basic information

Region (hg38): 22:41561010-41577741

Links

ENSG00000172346NCBI:27254OMIM:617689HGNC:30359Uniprot:Q9Y534AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
clinvar
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)2294107
22-41572003-C-T not specified Uncertain significance (May 07, 2024)3269725
22-41572053-G-A not specified Uncertain significance (Aug 02, 2021)2396430
22-41572064-G-C not specified Uncertain significance (Mar 23, 2022)3077957
22-41572080-G-A not specified Likely benign (Oct 25, 2022)3077954
22-41572092-C-T not specified Uncertain significance (Apr 12, 2022)2407638
22-41572093-G-A not specified Uncertain significance (Jul 02, 2024)2354858
22-41572113-C-G not specified Uncertain significance (Oct 29, 2024)3497504
22-41572129-G-C not specified Uncertain significance (Dec 01, 2022)2330829
22-41573722-C-T not specified Uncertain significance (Oct 10, 2023)3077956
22-41573774-C-T not specified Uncertain significance (Jun 21, 2023)2604903
22-41574765-A-G not specified Uncertain significance (Jun 22, 2023)2605124
22-41577353-C-T not specified Uncertain significance (Aug 02, 2023)2603075
22-41577355-C-T not specified Uncertain significance (Sep 02, 2024)3421396
22-41577368-C-G not specified Uncertain significance (Sep 18, 2024)3421399
22-41577431-C-T not specified Uncertain significance (Dec 27, 2023)3215837

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CSDC2protein_codingprotein_codingENST00000306149 316979
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.003120.613125688051256930.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7906181.00.7530.00000526956
Missense in Polyphen2334.2310.6719368
Synonymous-0.9724537.41.200.00000280323
Loss of Function0.44145.070.7892.52e-770

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005500.0000544
Finnish0.000.00
European (Non-Finnish)0.00002650.0000264
Middle Eastern0.00005500.0000544
South Asian0.00003270.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Csdc2
Phenotype

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