SPRYD4

SPRY domain containing 4

Basic information

Region (hg38): 12:56468578-56479708

Links

ENSG00000176422NCBI:283377HGNC:27468Uniprot:Q8WW59AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPRYD4 gene.

  • not_specified (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRYD4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000207344.4. 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
16
clinvar
1
clinvar
17
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 16 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SPRYD4protein_codingprotein_codingENST00000338146 22463
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.007910.7991257240231257470.0000915
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.809951200.7920.000006541324
Missense in Polyphen2245.6710.48171516
Synonymous0.1174647.00.9780.00000231438
Loss of Function1.0146.850.5843.03e-780

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003180.000318
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00007050.0000703
Middle Eastern0.00005440.0000544
South Asian0.00006530.0000653
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Pathway
miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

pRec
0.0721

Intolerance Scores

loftool
0.612
rvis_EVS
0.26
rvis_percentile_EVS
70.06

Haploinsufficiency Scores

pHI
0.0945
hipred
N
hipred_score
0.335
ghis
0.382

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.242

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Spryd4
Phenotype

Gene ontology

Biological process
biological_process
Cellular component
nucleus
Molecular function
molecular_function