SHLD3

shieldin complex subunit 3, the group of Shieldin complex

Basic information

Region (hg38): 5:65625026-65630928

Links

ENSG00000253251OMIM:618030HGNC:53826Uniprot:Q6ZNX1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SHLD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHLD3 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
0
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 0 0 0

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SHLD3protein_codingprotein_codingENST00000510585 16127
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.02060.91200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.08871200.7240.000005501626
Missense in Polyphen2031.30.63897438
Synonymous-0.05144342.61.010.00000200465
Loss of Function1.5649.050.4424.36e-7123

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the shieldin complex, which plays an important role in repair of DNA double-stranded breaks (DSBs). During G1 and S phase of the cell cycle, the complex functions downstream of TP53BP1 to promote non-homologous end joining (NHEJ) and suppress DNA end resection. Mediates various NHEJ-dependent processes including immunoglobulin class-switch recombination, and fusion of unprotected telomeres. {ECO:0000269|PubMed:29656893}.;

Haploinsufficiency Scores

pHI
hipred
hipred_score
ghis
0.406

Gene ontology

Biological process
DNA repair;positive regulation of isotype switching;negative regulation of double-strand break repair via homologous recombination;positive regulation of double-strand break repair via nonhomologous end joining
Cellular component
chromosome;site of double-strand break
Molecular function
protein binding