GOLM1

protein-coding

golgi membrane protein 1

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 transmembrane protein. It processes proteins synthesized in the rough endoplasmic reticulum and assists in the transport of protein cargo through the Golgi apparatus. The expression of this gene has been observed to be upregulated in response to viral infection. Alternatively spliced transcript variants encoding the same protein have been described for this gene. [provided by RefSeq, Sep 2009]

Previous symbols:

GOLPH2
C9orf155

MANE transcript

NM_016548.4

Inheritance

—

ClinVar variants

U:64B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr9:86,026,146-86,100,173

External References & Databases

Ensembl (ENSG00000135052)

Transcript & Mutation Effects

hg38 • Region Span ~74.0 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 GOLM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016548.4. 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	3 clinvar	6
missense			56 clinvar	6 clinvar	1 clinvar	63
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	64	8	4	76

Loading ClinVar variants...

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_016548.4	RefSeq	NP_057632.2	9	MANE Select
ENST00000388712.7	Ensembl	ENSP00000373364.3	9	MANE Select
NM_177937.3	RefSeq	NP_808800.1	9	Standard
ENST00000388711.7	Ensembl	ENSP00000373363.3	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein phosphorylation
Post-translational protein modification
Metabolism of proteins
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)

Biological Process

nucleus organization
regulation of lipid metabolic process
post-translational protein modification
cellular protein metabolic process

Molecular Function

protein binding

Cellular Component

extracellular space
endoplasmic reticulum lumen
Golgi apparatus
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000388712
Coding exons: 9
Length: 74028
Individuals with no LoFs: 125710
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125747
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.758	200	233	0.860	0.0000137	2629
Missense (PolyPhen)		47	53.046	0.88602		530
Synonymous	-0.191	96	93.7	1.03	0.00000586	746
Loss of Function	1.43	16	23.5	0.681	0.00000126	244

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Unknown. Cellular response protein to viral infection.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.764
RVIS EVS: 0.64
RVIS percentile EVS: 84.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.909

Gene Damage Prediction

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