GOLIM4

protein-coding

golgi integral membrane protein 4

Gene summary

The Golgi complex plays a key role in the sorting and modification of proteins exported from the endoplasmic reticulum. The protein encoded by this gene is a type II Golgi-resident protein. It may process proteins synthesized in the rough endoplasmic reticulum and assist in the transport of protein cargo through the Golgi apparatus. [provided by RefSeq, Jul 2008]

Previous symbols:

GOLPH4

MANE transcript

NM_014498.5

Inheritance

—

ClinVar variants

U:104B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr3:168,008,689-168,095,924

External References & Databases

Ensembl (ENSG00000173905)

Transcript & Mutation Effects

hg38 • Region Span ~87.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GOLIM4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014498.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar	1 clinvar	4
missense			99 clinvar	4 clinvar	1 clinvar	104
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	104	6	2	112

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014498.5	RefSeq	NP_055313.1	16	MANE Select
ENST00000470487.6	Ensembl	ENSP00000417354.1	16	MANE Select
NM_001308155.2	RefSeq	NP_001295084.1	15	Standard
ENST00000309027.4	Ensembl	ENSP00000309893.4	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Intra-Golgi traffic
Intra-Golgi and retrograde Golgi-to-ER traffic

Cellular Component

Golgi membrane
Golgi apparatus
Golgi lumen
cis-Golgi network
endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000470487
Coding exons: 16
Length: 87299
Individuals with no LoFs: 125706
Homozygous LoFs: 1
Heterozygous LoFs: 41
Defined: 125748
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.103	360	366	0.985	0.0000188	4629
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00023	0.00022	rare
South Asian	0.000065	0.000065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0939

Intolerance Scores

LoFtool: 0.168
RVIS EVS: -0.33
RVIS percentile EVS: 30.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0504

Gene Damage Prediction

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