PGGHG

protein-glucosylgalactosylhydroxylysine glucosidase, the group of Glycoside hydrolases

Basic information

Region (hg38): 11:289125-296107

Previous symbols: [ "ATHL1" ]

Links

ENSG00000142102 ∙ NCBI:80162 ∙ OMIM:617032 ∙ HGNC:26210 ∙ Uniprot:Q32M88 ∙ 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 PGGHG gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGGHG 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in PGGHG

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

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

Position	Type	Phenotype	Significance	ClinVar
11-289829-G-C		not specified	Uncertain significance (Jul 28, 2021)
11-290480-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-292049-G-A		not specified	Uncertain significance (Oct 06, 2021)
11-292060-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-292886-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-294397-G-A		not specified	Uncertain significance (Sep 27, 2021)
11-294461-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-294577-G-A		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGGHG	protein_coding	protein_coding	ENST00000409548	13	6973

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-14	0.379	125573	0	162	125735	0.000644

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.175	455	466	0.977	0.0000300	4708
Missense in Polyphen		134	163.9	0.81756		1731
Synonymous	-1.45	237	210	1.13	0.0000151	1565
Loss of Function	1.39	26	34.8	0.747	0.00000190	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000439	0.000439
Ashkenazi Jewish	0.000143	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000959	0.0000924
European (Non-Finnish)	0.000882	0.000853
Middle Eastern	0.000272	0.000272
South Asian	0.00141	0.00141
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolysis of glucose from the disaccharide unit linked to hydroxylysine residues of collagen and collagen-like proteins. {ECO:0000269|PubMed:26682924}.

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• rvis_EVS: -0.7
• rvis_percentile_EVS: 14.81

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.146
• ghis: 0.412

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pgghg

Gene ontology

• Biological process: carbohydrate metabolic process;trehalose catabolic process
• Cellular component: cell wall;cytosol
• Molecular function: alpha,alpha-trehalase activity;protein-glucosylgalactosylhydroxylysine glucosidase activity