ENOPH1

enolase-phosphatase 1, the group of HAD Asp-based non-protein phosphatases

Basic information

Region (hg38): 4:82430590-82461177

Links

ENSG00000145293 ∙ NCBI:58478 ∙ ∙ HGNC:24599 ∙ Uniprot:Q9UHY7 ∙ 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 ENOPH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENOPH1 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			5	1		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	5	2	0

Variants in ENOPH1

This is a list of pathogenic ClinVar variants found in the ENOPH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-82451062-T-G		not specified	Uncertain significance (Dec 19, 2022)
4-82451082-C-T		not specified	Uncertain significance (Feb 13, 2025)
4-82451120-G-T		not specified	Uncertain significance (Nov 16, 2022)
4-82451133-G-A		not specified	Uncertain significance (Oct 19, 2024)
4-82451186-C-T			Likely benign (May 04, 2018)
4-82451197-A-G		not specified	Uncertain significance (Jan 10, 2022)
4-82451232-C-T		not specified	Uncertain significance (Jan 24, 2023)
4-82460115-A-G		not specified	Likely benign (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENOPH1	protein_coding	protein_coding	ENST00000273920	6	30530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00612	0.975	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	85	147	0.577	0.00000745	1709
Missense in Polyphen		17	41.191	0.41272		540
Synonymous	-0.296	63	60.1	1.05	0.00000338	511
Loss of Function	2.06	6	14.4	0.415	8.32e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000277	0.000277
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK- MTPene). {ECO:0000255|HAMAP-Rule:MF_03117, ECO:0000269|PubMed:15843022}.
• Pathway: Cysteine and methionine metabolism - Homo sapiens (human);Methionine De Novo and Salvage Pathway;Metabolism of polyamines;Metabolism of amino acids and derivatives;Methionine salvage pathway;Metabolism;<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation;<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation;methionine salvage cycle III;Sulfur amino acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.459
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.0584
• hipred: N
• hipred_score: 0.379
• ghis: 0.681

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Enoph1

Gene ontology

• Biological process: dephosphorylation;L-methionine salvage from S-adenosylmethionine;L-methionine salvage from methylthioadenosine
• Cellular component: nucleus;cytosol
• Molecular function: magnesium ion binding;2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity;2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase activity;acireductone synthase activity