GADD45GIP1

GADD45G interacting protein 1

Basic information

Region (hg38): 19:12953119-12957223

Links

ENSG00000179271 ∙ NCBI:90480 ∙ OMIM:605162 ∙ HGNC:29996 ∙ Uniprot:Q8TAE8 ∙ 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 GADD45GIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GADD45GIP1 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			18	1	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	1

Variants in GADD45GIP1

This is a list of pathogenic ClinVar variants found in the GADD45GIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12954213-A-G		not specified	Uncertain significance (Dec 15, 2023)
19-12954234-C-G		not specified	Uncertain significance (Dec 28, 2024)
19-12954248-A-G		not specified	Likely benign (Jan 28, 2025)
19-12954254-G-A		not specified	Uncertain significance (Dec 17, 2023)
19-12954282-T-C			Benign (Mar 28, 2018)
19-12954312-G-A		not specified	Uncertain significance (Mar 07, 2025)
19-12954317-C-T		not specified	Uncertain significance (Oct 03, 2024)
19-12954350-T-C		not specified	Uncertain significance (Dec 14, 2021)
19-12954454-C-G		not specified	Uncertain significance (Feb 14, 2025)
19-12954497-T-C			Likely benign (Mar 01, 2025)
19-12954516-T-C		not specified	Uncertain significance (May 05, 2023)
19-12954525-C-G		not specified	Uncertain significance (Mar 30, 2024)
19-12956870-G-C		not specified	Uncertain significance (Oct 20, 2024)
19-12956923-G-T		not specified	Uncertain significance (Jan 29, 2024)
19-12956983-G-C		not specified	Uncertain significance (Jan 24, 2025)
19-12956993-A-C		not specified	Uncertain significance (Jan 01, 2025)
19-12956995-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-12956996-C-T		not specified	Uncertain significance (May 17, 2023)
19-12957010-G-T		not specified	Uncertain significance (Jan 24, 2025)
19-12957013-G-A		not specified	Uncertain significance (Feb 13, 2025)
19-12957016-G-A		not specified	Uncertain significance (Jul 19, 2023)
19-12957091-T-G		not specified	Uncertain significance (Nov 16, 2021)
19-12957124-G-A		not specified	Uncertain significance (Sep 19, 2023)
19-12957154-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-12957158-C-T		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GADD45GIP1	protein_coding	protein_coding	ENST00000316939	2	3079

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000103	0.597	125699	0	22	125721	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0409	122	121	1.01	0.00000639	1377
Missense in Polyphen		48	53.57	0.89603		601
Synonymous	0.630	48	53.9	0.891	0.00000256	479
Loss of Function	0.682	7	9.24	0.758	4.85e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000112	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000123
Middle Eastern	0.000168	0.000163
South Asian	0.0000988	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a negative regulator of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occurs also in the absence of GADD45 proteins. Acts as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity. May be involved in the hormone-mediated regulation of NR4A1 transcriptional activity. May play a role in mitochondrial protein synthesis.
• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Intolerance Scores

• loftool: 0.399
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.22

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.461
• ghis: 0.479

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.193

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gadd45gip1
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype

Gene ontology

• Biological process: viral process;mitochondrial translational elongation;mitochondrial translational termination;mitotic cell cycle arrest
• Cellular component: nucleus;mitochondrion;mitochondrial matrix;ribosome
• Molecular function: protein binding