CCSER1

coiled-coil serine rich protein 1

Basic information

Region (hg38): 4:90127394-91605295

Previous symbols: [ "FAM190A" ]

Links

ENSG00000184305NCBI:401145OMIM:618934HGNC:29349Uniprot:Q9C0I3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCSER1 gene.

  • not_specified (116 variants)
  • not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCSER1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001145065.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
112
clinvar
4
clinvar
1
clinvar
117
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 112 5 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCSER1protein_codingprotein_codingENST00000509176 101474379
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0007890.9991246160201246360.0000802
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.123974650.8540.00002395857
Missense in Polyphen127168.890.751982310
Synonymous0.2861701750.9730.000009441764
Loss of Function3.641235.40.3390.00000196471

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002280.000221
Ashkenazi Jewish0.0002010.000199
East Asian0.0001120.000111
Finnish0.000.00
European (Non-Finnish)0.00009030.0000885
Middle Eastern0.0001120.000111
South Asian0.00003760.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool
rvis_EVS
0.82
rvis_percentile_EVS
88.07

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.372
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ccser1
Phenotype