GID4

GID complex subunit 4 homolog

Basic information

Region (hg38): 17:18039408-18068405

Previous symbols: [ "C17orf39" ]

Links

ENSG00000141034 ∙ NCBI:79018 ∙ OMIM:617699 ∙ HGNC:28453 ∙ Uniprot:Q8IVV7 ∙ 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 GID4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GID4 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				1		1
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	18	2	0

Variants in GID4

This is a list of pathogenic ClinVar variants found in the GID4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18039426-G-A			Likely benign (Sep 02, 2019)
17-18039516-C-T		not specified	Uncertain significance (Sep 13, 2023)
17-18039528-G-T		not specified	Uncertain significance (Nov 08, 2022)
17-18039549-C-T		not specified	Uncertain significance (Mar 07, 2024)
17-18039552-G-A		not specified	Uncertain significance (Dec 15, 2024)
17-18039567-A-G		not specified	Uncertain significance (Oct 02, 2023)
17-18039571-A-C		not specified	Uncertain significance (Sep 16, 2021)
17-18039577-C-A		not specified	Uncertain significance (Aug 27, 2024)
17-18039610-G-T		not specified	Uncertain significance (Jun 17, 2024)
17-18039624-C-G		not specified	Uncertain significance (Sep 24, 2024)
17-18039628-C-A		not specified	Uncertain significance (Sep 27, 2024)
17-18039654-C-A		not specified	Uncertain significance (Feb 19, 2025)
17-18039678-C-T		not specified	Uncertain significance (Mar 17, 2023)
17-18039684-C-T		not specified	Uncertain significance (Aug 02, 2023)
17-18039822-A-T		not specified	Uncertain significance (Jul 05, 2024)
17-18039837-G-A		not specified	Uncertain significance (Feb 17, 2023)
17-18045157-C-A		not specified	Uncertain significance (May 24, 2023)
17-18045157-C-T		not specified	Uncertain significance (May 24, 2024)
17-18058912-A-C			Likely benign (Mar 01, 2023)
17-18058931-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-18058952-G-C		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GID4	protein_coding	protein_coding	ENST00000268719	6	29113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.921	0.0793	125722	0	6	125728	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	64	132	0.485	0.00000680	1904
Missense in Polyphen		14	46.13	0.30349		566
Synonymous	1.87	36	53.3	0.675	0.00000282	616
Loss of Function	3.02	1	12.5	0.0799	5.29e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-recognition subunit of the CTLH E3 ubiquitin- protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1 (Probable) (PubMed:29911972). Binds proteins and peptides with a Pro/N-degron consisting of an unmodified N-terminal Pro followed by a small residue, and has the highest affinity for the peptide Pro-Gly-Leu- Trp (PubMed:29632410). Binds peptides with an N-terminal sequence of the type Pro-[Ala,Gly]-[Leu,Met,Gln,Ser,Tyr]- [Glu,Gly,His,Ser,Val,Trp,Tyr]. Does not bind peptides with an acetylated N-terminal Pro residue (PubMed:29632410). {ECO:0000269|PubMed:29632410, ECO:0000269|PubMed:29911972, ECO:0000305}.

Haploinsufficiency Scores

• pHI: 0.487
• hipred: Y
• hipred_score: 0.550
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gid4

Gene ontology

• Biological process: protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process
• Cellular component: ubiquitin ligase complex
• Molecular function: ubiquitin protein ligase activity