PGAM4

phosphoglycerate mutase family member 4, the group of Bisphosphoglycerate phosphatases|Phosphoglycerate mutases

Basic information

Region (hg38): X:77967948-77969638

Links

ENSG00000226784 ∙ NCBI:441531 ∙ OMIM:300567 ∙ HGNC:21731 ∙ Uniprot:Q8N0Y7 ∙ 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 PGAM4 gene.

• Inborn genetic diseases (9 variants)
• not provided (2 variants)
• Menkes kinky-hair syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGAM4 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				1		1
missense			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	1

Variants in PGAM4

This is a list of pathogenic ClinVar variants found in the PGAM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-77968926-G-A		not specified	Uncertain significance (May 30, 2023)
X-77968990-C-T		not specified	Conflicting classifications of pathogenicity (Apr 27, 2022)
X-77969089-C-T		not specified	Uncertain significance (Jul 07, 2022)
X-77969227-T-C		not specified	Uncertain significance (Apr 27, 2023)
X-77969275-G-A		not specified	Uncertain significance (Sep 25, 2023)
X-77969353-T-C		not specified	Uncertain significance (Aug 17, 2022)
X-77969382-C-T		Menkes kinky-hair syndrome	Benign (May 28, 2019)
X-77969383-G-T		not specified	Uncertain significance (Jan 25, 2023)
X-77969410-T-A		not specified	Uncertain significance (Nov 21, 2022)
X-77969470-T-C		not specified	Uncertain significance (Jan 24, 2023)
X-77969516-G-A			Likely benign (Feb 01, 2023)
X-77969598-C-T		not specified	Uncertain significance (Jan 24, 2024)
X-77969611-G-A		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGAM4	protein_coding	protein_coding	ENST00000458128	1	1678

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.199	107	113	0.947	0.00000997	1663
Missense in Polyphen		25	25.982	0.96222		543
Synonymous	1.00	41	50.0	0.820	0.00000460	514
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.294
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.347
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.573

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgam1

Gene ontology

• Biological process: glycolytic process;positive regulation of flagellated sperm motility
• Cellular component: extracellular exosome;sperm principal piece
• Molecular function: bisphosphoglycerate mutase activity;phosphoglycerate mutase activity;hydrolase activity