CCDC172

coiled-coil domain containing 172

Basic information

Region (hg38): 10:116324448-116380029

Previous symbols: [ "C10orf96" ]

Links

ENSG00000182645NCBI:374355HGNC:30524Uniprot:P0C7W6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC172 gene.

  • not_specified (35 variants)
  • Meckel-Gruber_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC172 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198515.3. 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
0
missense
32
clinvar
3
clinvar
35
nonsense
0
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 0 0 33 3 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCDC172protein_codingprotein_codingENST00000333254 855602
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00003730.8391257140321257460.000127
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.06161161180.9840.000005471748
Missense in Polyphen1623.4780.68148348
Synonymous0.8293137.50.8280.00000178371
Loss of Function1.33914.40.6236.48e-7211

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003480.000339
Ashkenazi Jewish0.000.00
East Asian0.0003400.000326
Finnish0.000.00
European (Non-Finnish)0.0001570.000149
Middle Eastern0.0003400.000326
South Asian0.00006800.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool
rvis_EVS
-0.05
rvis_percentile_EVS
49.76

Haploinsufficiency Scores

pHI
0.0679
hipred
N
hipred_score
0.173
ghis
0.411

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
Ccdc172
Phenotype

Gene ontology

Biological process
Cellular component
cytoplasm;sperm midpiece
Molecular function
protein binding