PGAP6

post-GPI attachment to proteins 6, the group of TMEM8 family

Basic information

Region (hg38): 16:370788-387113

Previous symbols: [ "TMEM6", "TMEM8", "TMEM8A" ]

Links

ENSG00000129925

∙ NCBI:58986 ∙ OMIM:619342 ∙ HGNC:17205 ∙ Uniprot:Q9HCN3 ∙ 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 PGAP6 gene.

not_specified (183 variants)
not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGAP6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021259.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			169 clinvar	16 clinvar		185
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	169	17	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGAP6	protein_coding	protein_coding	ENST00000431232	13	16341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.37e-10	0.940	125402	0	154	125556	0.000613

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.13	565	494	1.14	0.0000340	4898
Missense in Polyphen		201	180.51	1.1135		1812
Synonymous	-2.30	273	229	1.19	0.0000176	1639
Loss of Function	2.00	20	32.3	0.620	0.00000156	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000817	0.000805
Ashkenazi Jewish	0.000100	0.0000994
East Asian	0.00104	0.00103
Finnish	0.00108	0.00102
European (Non-Finnish)	0.000453	0.000423
Middle Eastern	0.00104	0.00103
South Asian	0.00151	0.00134
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in the lipid remodeling steps of GPI-anchor maturation. Lipid remodeling steps consist in the generation of 2 saturated fatty chains at the sn-2 position of GPI-anchor proteins (GPI-AP). Has phospholipase A2 activity that removes an acyl-chain at the sn-2 position of GPI-anchors during the remodeling of GPI. Required for the shedding of the GPI-AP TDGF1, but not CFC1, at the cell surface. Shedding of TDGF1 modulates Nodal signaling by allowing soluble TDGF1 to act as a Nodal coreceptor on other cells (PubMed:27881714). Also indirectly involved in the translocation of RAC1 from the cytosol to the plasma membrane by maintaining the steady state amount of CAV1-enriched plasma membrane subdomains, stabilizing RAC1 at the plasma membrane (PubMed:27835684). In contrast to myomaker (TMEM8C), has no fusogenic activity (PubMed:26858401). {ECO:0000269|PubMed:26858401, ECO:0000269|PubMed:27835684, ECO:0000269|PubMed:27881714}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

loftool: 0.807
rvis_EVS: 0.12
rvis_percentile_EVS: 62.4

Haploinsufficiency Scores

pHI: 0.174
hipred: N
hipred_score: 0.383
ghis: 0.476

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.176

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tmem8
Phenotype: 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); embryo phenotype;

Gene ontology

Biological process: biological_process
Cellular component: lysosomal membrane;plasma membrane;integral component of plasma membrane;extracellular exosome
Molecular function: molecular_function;phospholipase A2 activity;protein binding;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)