SHLD1

shieldin complex subunit 1, the group of Shieldin complex

Basic information

Region (hg38): 20:5750393-5864395

Previous symbols: [ "C20orf196" ]

Links

ENSG00000171984 ∙ NCBI:149840 ∙ OMIM:618028 ∙ HGNC:26318 ∙ Uniprot:Q8IYI0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SHLD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHLD1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in SHLD1

This is a list of pathogenic ClinVar variants found in the SHLD1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-5772960-A-G		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHLD1	protein_coding	protein_coding	ENST00000303142	2	113520

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.166	0.778	125726	0	16	125742	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.479	97	111	0.872	0.00000571	1351
Missense in Polyphen		27	27.744	0.97319		371
Synonymous	-0.199	47	45.3	1.04	0.00000253	388
Loss of Function	1.57	2	6.24	0.320	2.63e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000276
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000326	0.000326
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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}.

Intolerance Scores

• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.4

Haploinsufficiency Scores

• pHI: 0.0689
• hipred: N
• hipred_score: 0.146
• ghis: 0.378

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Shld1

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