GOLM2

golgi membrane protein 2

Basic information

Region (hg38): 15:44288718-44415758

Previous symbols: [ "CASC4" ]

Links

ENSG00000166734 ∙ NCBI:113201 ∙ ∙ HGNC:24892 ∙ Uniprot:Q6P4E1 ∙ 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 GOLM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLM2 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			27	1	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	1

Variants in GOLM2

This is a list of pathogenic ClinVar variants found in the GOLM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-44289220-A-G		not specified	Uncertain significance (Jan 20, 2023)
15-44289229-A-G		not specified	Uncertain significance (Feb 15, 2023)
15-44289255-A-G		not specified	Uncertain significance (Jan 26, 2022)
15-44289261-A-C		not specified	Uncertain significance (Aug 22, 2023)
15-44289294-G-T		not specified	Uncertain significance (May 05, 2023)
15-44289326-G-C		not specified	Uncertain significance (Jun 02, 2023)
15-44322987-C-T		not specified	Uncertain significance (Jan 17, 2024)
15-44328714-C-T		not specified	Uncertain significance (Sep 13, 2023)
15-44328732-C-T		not specified	Uncertain significance (Sep 06, 2022)
15-44328752-C-A		not specified	Uncertain significance (Dec 30, 2023)
15-44328772-G-T		not specified	Uncertain significance (Dec 21, 2023)
15-44332028-C-A		not specified	Uncertain significance (Jan 08, 2024)
15-44332040-A-T		not specified	Uncertain significance (Sep 27, 2021)
15-44337776-A-G		not specified	Uncertain significance (Oct 03, 2023)
15-44337877-C-A		not specified	Uncertain significance (Aug 30, 2021)
15-44337899-A-C			Benign (Dec 14, 2017)
15-44338275-A-G		not specified	Uncertain significance (Jan 07, 2022)
15-44338300-T-G		not specified	Uncertain significance (Jan 23, 2024)
15-44338309-T-A		not specified	Uncertain significance (Jun 29, 2022)
15-44379722-C-T		not specified	Likely benign (Jan 06, 2023)
15-44379749-C-G		not specified	Uncertain significance (Dec 15, 2023)
15-44380854-C-T		not specified	Uncertain significance (Feb 15, 2023)
15-44380942-G-T		not specified	Conflicting classifications of pathogenicity (Feb 10, 2023)
15-44380943-G-A		not specified	Uncertain significance (May 27, 2022)
15-44380968-T-C		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLM2	protein_coding	protein_coding	ENST00000299957	10	127030

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000716	0.996	125724	0	15	125739	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	186	235	0.792	0.0000111	2885
Missense in Polyphen		47	73.969	0.63541		963
Synonymous	1.76	68	89.2	0.763	0.00000438	791
Loss of Function	2.53	11	24.5	0.448	0.00000129	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000274
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000715	0.0000703
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.113
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.0920
• hipred: Y
• hipred_score: 0.541
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.953

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Casc4
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Cellular component: Golgi apparatus;integral component of membrane