SPECC1

sperm antigen with calponin homology and coiled-coil domains 1

Basic information

Region (hg38): 17:20008865-20319026

Previous symbols: [ "CYTSB" ]

Links

ENSG00000128487NCBI:92521OMIM:608793HGNC:30615Uniprot:Q5M775AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPECC1 gene.

  • not_specified (146 variants)
  • not_provided (3 variants)
  • Myoepithelial_tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPECC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001243439.2. 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
1
clinvar
139
clinvar
8
clinvar
148
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 1 139 9 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SPECC1protein_codingprotein_codingENST00000261503 14309683
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0008680.9991256780701257480.000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1886196061.020.00003516961
Missense in Polyphen191222.440.858642677
Synonymous-1.702702371.140.00001382124
Loss of Function4.231444.40.3150.00000228561

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005930.000591
Ashkenazi Jewish0.0002980.000298
East Asian0.0003270.000326
Finnish0.00009250.0000924
European (Non-Finnish)0.0002300.000229
Middle Eastern0.0003270.000326
South Asian0.0004250.000425
Other0.0004900.000489

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.0875

Intolerance Scores

loftool
rvis_EVS
-1.19
rvis_percentile_EVS
5.89

Haploinsufficiency Scores

pHI
0.0963
hipred
N
hipred_score
0.474
ghis
0.527

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Specc1
Phenotype

Zebrafish Information Network

Gene name
specc1
Affected structure
hyosymplectic cartilage
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
actin cytoskeleton organization
Cellular component
nucleus;microtubule organizing center;membrane;filamentous actin
Molecular function