GOLM1

golgi membrane protein 1

Basic information

Region (hg38): 9:86026146-86100173

Previous symbols: [ "GOLPH2", "C9orf155" ]

Links

ENSG00000135052 ∙ NCBI:51280 ∙ OMIM:606804 ∙ HGNC:15451 ∙ Uniprot:Q8NBJ4 ∙ 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 GOLM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLM1 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				2	2	4
missense			21	1	1	23
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	21	3	3

Variants in GOLM1

This is a list of pathogenic ClinVar variants found in the GOLM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-86027833-C-T		not specified	Uncertain significance (Nov 14, 2024)
9-86027852-G-A		not specified	Uncertain significance (Sep 13, 2023)
9-86027879-C-A		not specified	Uncertain significance (Mar 25, 2024)
9-86033287-A-G		not specified	Uncertain significance (Aug 27, 2024)
9-86033359-T-C		not specified	Uncertain significance (Oct 26, 2022)
9-86033395-C-T		not specified	Uncertain significance (Feb 04, 2022)
9-86035392-C-T		not specified	Uncertain significance (Oct 30, 2023)
9-86035405-G-A			Benign (Mar 29, 2018)
9-86035513-G-A			Benign (Jun 27, 2018)
9-86035513-G-C		not specified	Uncertain significance (Mar 20, 2023)
9-86035556-C-T		not specified	Likely benign (Jul 08, 2022)
9-86035558-G-A			Likely benign (Dec 01, 2022)
9-86035580-T-A		not specified	Uncertain significance (Nov 11, 2024)
9-86035592-T-G		not specified	Uncertain significance (Jun 26, 2024)
9-86036354-C-G		not specified	Uncertain significance (May 31, 2023)
9-86036423-G-A		not specified	Uncertain significance (Oct 25, 2024)
9-86036426-C-T		not specified	Uncertain significance (Nov 15, 2021)
9-86036434-T-A		not specified	Uncertain significance (Sep 23, 2023)
9-86036450-C-G		not specified	Uncertain significance (Jan 26, 2022)
9-86040753-C-T		not specified	Uncertain significance (Jun 04, 2024)
9-86040755-T-C		not specified	Uncertain significance (Apr 19, 2023)
9-86040756-T-C		not specified	Uncertain significance (Mar 17, 2023)
9-86046467-C-T			Benign (Dec 31, 2019)
9-86046512-T-A		not specified	Uncertain significance (Nov 03, 2023)
9-86046538-C-G			Benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLM1	protein_coding	protein_coding	ENST00000388712	9	74028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.62e-9	0.754	125710	0	37	125747	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.758	200	233	0.860	0.0000137	2629
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000211
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000218	0.000217
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Unknown. Cellular response protein to viral infection.
• Pathway: 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) (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.764
• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.05

Haploinsufficiency Scores

• pHI: 0.396
• hipred: N
• hipred_score: 0.198
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.909

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golm1
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; renal/urinary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: nucleus organization;regulation of lipid metabolic process;post-translational protein modification;cellular protein metabolic process
• Cellular component: extracellular space;endoplasmic reticulum lumen;Golgi apparatus;integral component of plasma membrane
• Molecular function: protein binding