GOLIM4

golgi integral membrane protein 4

Basic information

Region (hg38): 3:168008689-168095924

Previous symbols: [ "GOLPH4" ]

Links

ENSG00000173905 ∙ NCBI:27333 ∙ OMIM:606805 ∙ HGNC:15448 ∙ Uniprot:O00461 ∙ 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 GOLIM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLIM4 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			53	2	1	56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	53	3	1

Variants in GOLIM4

This is a list of pathogenic ClinVar variants found in the GOLIM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-168010286-G-C		not specified	Uncertain significance (Aug 10, 2024)
3-168010300-G-A		not specified	Uncertain significance (May 14, 2024)
3-168010346-G-A		not specified	Uncertain significance (Aug 05, 2024)
3-168010354-C-T			Uncertain significance (Apr 29, 2021)
3-168010367-G-A		not specified	Uncertain significance (May 26, 2023)
3-168010767-C-A		not specified	Uncertain significance (Dec 20, 2024)
3-168010813-T-C		not specified	Uncertain significance (Jan 20, 2025)
3-168024952-A-C		not specified	Uncertain significance (Jun 28, 2024)
3-168024959-T-C		not specified	Uncertain significance (Jul 13, 2021)
3-168024968-T-C		not specified	Uncertain significance (Jun 12, 2023)
3-168024969-T-G		not specified	Uncertain significance (Jan 07, 2022)
3-168025023-C-T		not specified	Uncertain significance (May 05, 2023)
3-168025074-T-G		not specified	Uncertain significance (Dec 04, 2024)
3-168025082-T-A		not specified	Uncertain significance (Oct 03, 2023)
3-168027748-C-T		not specified	Likely benign (Jan 22, 2025)
3-168027760-G-A		not specified	Uncertain significance (Sep 20, 2023)
3-168027775-G-C		not specified	Uncertain significance (Jan 01, 2025)
3-168027781-G-T		not specified	Uncertain significance (Apr 09, 2024)
3-168027789-C-T		not specified	Uncertain significance (Feb 26, 2025)
3-168027810-T-C		not specified	Uncertain significance (May 01, 2023)
3-168027814-G-C		not specified	Uncertain significance (Jan 10, 2023)
3-168027834-T-C		not specified	Uncertain significance (Apr 04, 2024)
3-168027842-C-A			Benign (May 14, 2018)
3-168029261-T-C		not specified	Uncertain significance (Oct 28, 2024)
3-168029279-A-G		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLIM4	protein_coding	protein_coding	ENST00000470487	16	87299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.97e-11	0.999	125706	1	41	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.103	360	366	0.985	0.0000188	4629
Missense in Polyphen		132	137.14	0.96254		1967
Synonymous	-0.294	139	135	1.03	0.00000691	1167
Loss of Function	3.05	25	47.7	0.524	0.00000245	525

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000273	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000230	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in endosome to Golgi protein trafficking; mediates protein transport along the late endosome-bypass pathway from the early endosome to the Golgi. {ECO:0000269|PubMed:15331763}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Intra-Golgi traffic;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.0939

Intolerance Scores

• loftool: 0.168
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.82

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.445
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0504

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golim4

Gene ontology

• Cellular component: Golgi membrane;Golgi apparatus;Golgi lumen;cis-Golgi network;endosome membrane;membrane;integral component of membrane;transport vesicle;endocytic vesicle;Golgi cisterna membrane