GOLPH3L

golgi phosphoprotein 3 like

Basic information

Region (hg38): 1:150646230-150697154

Links

ENSG00000143457NCBI:55204OMIM:612208HGNC:24882Uniprot:Q9H4A5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GOLPH3L gene.

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.

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
16
clinvar
1
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 16 1 0

Variants in GOLPH3L

This is a list of pathogenic ClinVar variants found in the GOLPH3L region.

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

Position Type Phenotype Significance ClinVar
1-150648511-A-G not specified Uncertain significance (Feb 12, 2024)3100980
1-150648529-C-T not specified Uncertain significance (Oct 09, 2024)3521305
1-150648530-G-A not specified Uncertain significance (Mar 07, 2024)3100979
1-150648550-C-T not specified Uncertain significance (Mar 06, 2023)2462966
1-150648551-G-A not specified Uncertain significance (Oct 02, 2023)3100978
1-150648565-T-C not specified Uncertain significance (Jul 30, 2024)3521307
1-150648598-G-T not specified Uncertain significance (Dec 21, 2022)2338823
1-150648640-A-C not specified Uncertain significance (Jun 21, 2023)2600630
1-150661827-T-C not specified Uncertain significance (Oct 12, 2022)2226550
1-150661866-G-C not specified Uncertain significance (Aug 04, 2023)2616481
1-150663639-T-C not specified Uncertain significance (Dec 11, 2023)3100976
1-150663666-G-A not specified Uncertain significance (Aug 03, 2022)2384891
1-150663681-A-C not specified Uncertain significance (Aug 14, 2023)2618387
1-150663684-C-T not specified Uncertain significance (Jun 23, 2023)2588499
1-150663691-G-A not specified Uncertain significance (Sep 09, 2024)3521306
1-150663737-G-C not specified Uncertain significance (Sep 16, 2021)2348037
1-150694693-A-G not specified Uncertain significance (Apr 28, 2023)2509478
1-150694786-T-G not specified Uncertain significance (Oct 30, 2023)3100977
1-150694802-T-C not specified Likely benign (Jun 18, 2021)2233656
1-150694807-G-C not specified Uncertain significance (Dec 14, 2022)2334713

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GOLPH3Lprotein_codingprotein_codingENST00000271732 450930
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00001260.8431257180291257470.000115
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9421281620.7920.000009051845
Missense in Polyphen3756.8410.65094676
Synonymous0.5685257.50.9050.00000261581
Loss of Function1.381015.90.6270.00000124139

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002470.000246
Ashkenazi Jewish0.000.00
East Asian0.0002180.000217
Finnish0.0001850.000185
European (Non-Finnish)0.0001150.000114
Middle Eastern0.0002180.000217
South Asian0.00006560.0000653
Other0.0003280.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Golph3l
Phenotype

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