GOLGA6L2

golgin A6 family like 2, the group of Golgin related

Basic information

Region (hg38): 15:23439038-23447243

Links

ENSG00000174450 ∙ NCBI:283685 ∙ ∙ HGNC:26695 ∙ Uniprot:Q8N9W4 ∙ 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 GOLGA6L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA6L2 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				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in GOLGA6L2

This is a list of pathogenic ClinVar variants found in the GOLGA6L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-23440127-A-G			Likely benign (Apr 01, 2023)
15-23440461-T-C			Uncertain significance (-)
15-23440478-T-C			Uncertain significance (-)
15-23440500-C-T			Uncertain significance (-)
15-23440773-A-C			Uncertain significance (-)
15-23440775-C-T			Uncertain significance (-)
15-23440775-C-CCCGCATCTTCTCCTCCTGCTT			Uncertain significance (-)
15-23441399-T-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA6L2	protein_coding	protein_coding	ENST00000567107	8	7737

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000106	0.570	123729	0	64	123793	0.000259

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	432	469	0.922	0.0000275	5655
Missense in Polyphen		50	59.843	0.83551		888
Synonymous	1.01	150	167	0.900	0.00000975	1643
Loss of Function	0.908	11	14.8	0.745	8.09e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00226	0.00202
Ashkenazi Jewish	0.00	0.00
East Asian	0.000387	0.000384
Finnish	0.0000645	0.0000498
European (Non-Finnish)	0.000131	0.000124
Middle Eastern	0.000387	0.000384
South Asian	0.000197	0.000196
Other	0.000168	0.000165

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.399

Essentials

• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High