GOLPH3

golgi phosphoprotein 3

Basic information

Region (hg38): 5:32124716-32174319

Links

ENSG00000113384

∙ NCBI:64083 ∙ OMIM:612207 ∙ HGNC:15452 ∙ Uniprot:Q9H4A6 ∙ 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 GOLPH3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLPH3 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				2 clinvar		2
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in GOLPH3

This is a list of pathogenic ClinVar variants found in the GOLPH3 region.

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

Position	Phenotype	Significance	ClinVar
5-32126216-T-G	not specified	Uncertain significance (Oct 25, 2023)	3100974
5-32126228-G-A	not specified	Uncertain significance (Mar 19, 2024)	3281973
5-32126292-C-T	not specified	Uncertain significance (Aug 07, 2024)	3521303
5-32126304-G-A	not specified	Uncertain significance (Nov 03, 2023)	3100973
5-32126315-G-A	not specified	Uncertain significance (Dec 13, 2021)	2266560
5-32126329-C-A	not specified	Uncertain significance (Nov 18, 2022)	2328153
5-32126346-G-A	not specified	Uncertain significance (Dec 15, 2022)	2335703
5-32126349-C-G	not specified	Uncertain significance (Aug 02, 2021)	2240434
5-32126368-G-A		Likely benign (Feb 01, 2023)	2655384
5-32126418-G-A	not specified	Uncertain significance (Apr 17, 2024)	3281972
5-32126468-A-G	not specified	Uncertain significance (Nov 13, 2024)	3521304
5-32126475-G-A	not specified	Uncertain significance (Oct 13, 2023)	3100972
5-32126613-A-G		Likely benign (Feb 01, 2023)	2655385
5-32135658-C-T	not specified	Uncertain significance (Jan 27, 2025)	3854742
5-32135670-T-A	not specified	Uncertain significance (Apr 18, 2024)	3281974
5-32143822-A-G	not specified	Uncertain significance (May 01, 2023)	2529012
5-32173875-C-A	not specified	Uncertain significance (Feb 20, 2025)	3854741

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLPH3	protein_coding	protein_coding	ENST00000265070	4	49647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.236	0.758	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	103	161	0.638	0.00000895	1914
Missense in Polyphen		26	56.044	0.46392		746
Synonymous	1.31	50	63.2	0.791	0.00000338	583
Loss of Function	2.35	3	11.7	0.257	5.87e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000124	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.000124	0.000109
South Asian	0.000425	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Phosphatidylinositol-4-phosphate-binding protein that links Golgi membranes to the cytoskeleton and may participate in the tensile force required for vesicle budding from the Golgi. Thereby, may play a role in Golgi membrane trafficking and could indirectly give its flattened shape to the Golgi apparatus. May also bind to the coatomer to regulate Golgi membrane trafficking. May play a role in anterograde transport from the Golgi to the plasma membrane and regulate secretion. Has also been involved in the control of the localization of Golgi enzymes through interaction with their cytoplasmic part. May play an indirect role in cell migration. Has also been involved in the modulation of mTOR signaling. May also be involved in the regulation of mitochondrial lipids biosynthesis. {ECO:0000269|PubMed:16263763, ECO:0000269|PubMed:19553991, ECO:0000269|PubMed:19837035, ECO:0000269|PubMed:22745132, ECO:0000269|PubMed:23027862, ECO:0000269|PubMed:23345592, ECO:0000269|PubMed:23500462}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

loftool: 0.263
rvis_EVS: -0.36
rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

pHI: 0.793
hipred: N
hipred_score: 0.483
ghis: 0.604

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.714

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Golph3
Phenotype

Gene ontology

Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi organization;cell population proliferation;glycoprotein biosynthetic process;protein secretion;gene expression;regulation of mitochondrion organization;cell migration;lamellipodium assembly;positive regulation of TOR signaling;Golgi to plasma membrane protein transport;negative regulation of apoptotic process;protein retention in Golgi apparatus;Golgi vesicle budding;positive regulation of protein secretion;leukocyte tethering or rolling;cell adhesion molecule production;Golgi ribbon formation;asymmetric Golgi ribbon formation
Cellular component: mitochondrion;mitochondrial intermembrane space;endosome;Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;Golgi cisterna;Golgi cisterna membrane;intracellular membrane-bounded organelle
Molecular function: protein binding;enzyme binding;phosphatidylinositol-4-phosphate binding