GOLPH3L

golgi phosphoprotein 3 like

Basic information

Region (hg38): 1:150646230-150697154

Links

ENSG00000143457 ∙ NCBI:55204 ∙ OMIM:612208 ∙ HGNC:24882 ∙ Uniprot:Q9H4A5 ∙ 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 GOLPH3L gene.

• not_specified (30 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLPH3L gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018178.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLPH3L	protein_coding	protein_coding	ENST00000271732	4	50930

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000126	0.843	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.942	128	162	0.792	0.00000905	1845
Missense in Polyphen		37	56.841	0.65094		676
Synonymous	0.568	52	57.5	0.905	0.00000261	581
Loss of Function	1.38	10	15.9	0.627	0.00000124	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000247	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000218	0.000217
South Asian	0.0000656	0.0000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatidylinositol-4-phosphate-binding protein that may antagonize the action of GOLPH3 which is required for the process of vesicle budding at the Golgi and anterograde transport to the plasma membrane. {ECO:0000269|PubMed:23345592}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.376
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.368
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.690

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golph3l

Gene ontology

• Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi organization;Golgi to plasma membrane protein transport;Golgi vesicle budding;positive regulation of protein secretion
• Cellular component: Golgi membrane;trans-Golgi network;cytosol;Golgi cisterna;Golgi cisterna membrane;trans-Golgi network membrane
• Molecular function: protein binding;phosphatidylinositol-4-phosphate binding