PGAM4

protein-coding

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

Gene summary

This intronless gene appears to have arisen from a retrotransposition event, yet it is thought to be an expressed, protein-coding gene. The encoded protein is a member of the phosphoglycerate mutase family, a set of enzymes that catalyze the transfer of a phosphate group from 3-phosphoglycerate to 2-phosphoglycerate. [provided by RefSeq, May 2010]

MANE transcript

NM_001029891.3

Inheritance

—

ClinVar variants

U:34B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:77,967,949-77,969,638

External References & Databases

Ensembl (ENSG00000226784)

Transcript & Mutation Effects

hg38 • Region Span ~1.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PGAM4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001029891.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			34 clinvar	1 clinvar		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	5	0	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001029891.3	RefSeq	NP_001025062.1	1	MANE Select
ENST00000458128.3	Ensembl	ENSP00000412189.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

glycolytic process
positive regulation of flagellated sperm motility

Molecular Function

bisphosphoglycerate mutase activity
phosphoglycerate mutase activity
hydrolase activity

Cellular Component

extracellular exosome
sperm principal piece

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000458128
Coding exons: 1
Length: 1678

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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.156

Intolerance Scores

LoFtool: 0.294
RVIS EVS: 0.42
RVIS percentile EVS: 76.81

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.573

Gene Damage Prediction

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