SUMF2
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Also known as DKFZp566I1024
Summary
SUMF2 (sulfatase modifying factor 2, HGNC:20415) is a protein-coding gene on chromosome 7p11.2, encoding Inactive C-alpha-formylglycine-generating enzyme 2 (Q8NBJ7). Lacks formylglycine generating activity and is unable to convert newly synthesized inactive sulfatases to their active form.
The catalytic sites of sulfatases are only active if they contain a unique amino acid, C-alpha-formylglycine (FGly). The FGly residue is posttranslationally generated from a cysteine by enzymes with FGly-generating activity. The gene described in this record is a member of the sulfatase-modifying factor family and encodes a protein with a DUF323 domain that localizes to the lumen of the endoplasmic reticulum. This protein has low levels of FGly-generating activity but can heterodimerize with another family member - a protein with high levels of FGly-generating activity. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.
Source: NCBI Gene 25870 — RefSeq curated summary.
At a glance
- GWAS associations: 4
- Clinical variants (ClinVar): 123 total — 1 pathogenic
- MANE Select transcript:
NM_015411
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:20415 |
| Approved symbol | SUMF2 |
| Name | sulfatase modifying factor 2 |
| Location | 7p11.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | DKFZp566I1024 |
| Ensembl gene | ENSG00000129103 |
| Ensembl biotype | protein_coding |
| OMIM | 607940 |
| Entrez | 25870 |
Gene structure
Transcript identifiers
Ensembl transcripts: 30 — 20 protein_coding, 5 nonsense_mediated_decay, 5 retained_intron
ENST00000275607, ENST00000342190, ENST00000395435, ENST00000395436, ENST00000413756, ENST00000413952, ENST00000423763, ENST00000434526, ENST00000436782, ENST00000437307, ENST00000438133, ENST00000447501, ENST00000451338, ENST00000452216, ENST00000461912, ENST00000483327, ENST00000498777, ENST00000529457, ENST00000531229, ENST00000650735, ENST00000651354, ENST00000651586, ENST00000652303, ENST00000911043, ENST00000911044, ENST00000911045, ENST00000911046, ENST00000966154, ENST00000966155, ENST00000966156
RefSeq mRNA: 9 — MANE Select: NM_015411
NM_001042468, NM_001042469, NM_001042470, NM_001130069, NM_001146333, NM_001366647, NM_001366648, NM_001366649, NM_015411
CCDS: CCDS43588, CCDS43589, CCDS47589, CCDS55111, CCDS5524, CCDS94107
Canonical transcript exons
ENST00000434526 — 9 exons
| Exon | Start | End |
|---|---|---|
| ENSE00003565405 | 56078102 | 56078186 |
| ENSE00003568149 | 56076834 | 56076889 |
| ENSE00003598740 | 56079528 | 56080670 |
| ENSE00003642638 | 56074586 | 56074736 |
| ENSE00003645259 | 56072997 | 56073111 |
| ENSE00003672921 | 56078364 | 56078508 |
| ENSE00003683911 | 56074174 | 56074218 |
| ENSE00003690403 | 56068482 | 56068638 |
| ENSE00003901661 | 56064286 | 56064378 |
Expression profiles
Bgee: expression breadth ubiquitous, 246 present calls, max score 98.59.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 73.0856 / max 302.6621, expressed in 1826 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 78774 | 72.0729 | 1826 |
| 78776 | 0.9777 | 640 |
| 204451 | 0.0350 | 7 |
Top tissues by expression
251 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| right uterine tube | UBERON:0001302 | 98.59 | gold quality |
| stromal cell of endometrium | CL:0002255 | 98.32 | gold quality |
| body of pancreas | UBERON:0001150 | 98.23 | gold quality |
| gall bladder | UBERON:0002110 | 97.87 | gold quality |
| endocervix | UBERON:0000458 | 97.86 | gold quality |
| islet of Langerhans | UBERON:0000006 | 97.82 | gold quality |
| pancreas | UBERON:0001264 | 97.82 | gold quality |
| pancreatic ductal cell | CL:0002079 | 97.54 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 97.47 | gold quality |
| right adrenal gland | UBERON:0001233 | 97.46 | gold quality |
| mucosa of stomach | UBERON:0001199 | 97.29 | gold quality |
| rectum | UBERON:0001052 | 97.26 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 97.24 | gold quality |
| right lung | UBERON:0002167 | 97.21 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 97.21 | gold quality |
| minor salivary gland | UBERON:0001830 | 97.19 | gold quality |
| metanephros cortex | UBERON:0010533 | 97.19 | gold quality |
| left adrenal gland | UBERON:0001234 | 97.18 | gold quality |
| right coronary artery | UBERON:0001625 | 97.18 | gold quality |
| skin of leg | UBERON:0001511 | 97.13 | gold quality |
| right ovary | UBERON:0002118 | 97.12 | gold quality |
| left ovary | UBERON:0002119 | 97.08 | gold quality |
| ectocervix | UBERON:0012249 | 97.08 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 97.07 | gold quality |
| body of stomach | UBERON:0001161 | 97.06 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 97.04 | gold quality |
| body of uterus | UBERON:0009853 | 97.03 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 96.99 | gold quality |
| skin of abdomen | UBERON:0001416 | 96.98 | gold quality |
| thoracic aorta | UBERON:0001515 | 96.95 | gold quality |
Single-cell (SCXA)
Detected in 3 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-7303 | no | 1080.37 |
| E-MTAB-4850 | no | 591.63 |
| E-ANND-3 | no | 0.00 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
66 targeting SUMF2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-188-3P | 100.00 | 68.76 | 1240 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-6870-5P | 99.99 | 68.55 | 2115 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-4723-5P | 99.97 | 68.70 | 2034 |
| HSA-MIR-5698 | 99.97 | 68.49 | 2029 |
| HSA-MIR-7111-5P | 99.97 | 68.48 | 2062 |
| HSA-MIR-6780A-5P | 99.88 | 66.69 | 2776 |
| HSA-MIR-1273H-5P | 99.77 | 66.32 | 2471 |
| HSA-MIR-4306 | 99.72 | 70.50 | 3630 |
| HSA-MIR-1200 | 99.71 | 70.42 | 1838 |
| HSA-MIR-30B-3P | 99.70 | 65.76 | 2325 |
| HSA-MIR-3689A-3P | 99.70 | 65.73 | 2306 |
| HSA-MIR-3689B-3P | 99.70 | 65.71 | 2311 |
| HSA-MIR-3689C | 99.70 | 65.71 | 2311 |
| HSA-MIR-6779-5P | 99.70 | 65.76 | 2363 |
| HSA-MIR-6134 | 99.63 | 65.68 | 1537 |
| HSA-MIR-4261 | 99.59 | 70.30 | 3415 |
| HSA-MIR-7106-5P | 99.53 | 67.47 | 3574 |
| HSA-MIR-4441 | 99.49 | 66.56 | 3216 |
| HSA-MIR-3123 | 99.47 | 67.15 | 2693 |
| HSA-MIR-3612 | 99.45 | 66.02 | 1333 |
| HSA-MIR-650 | 99.45 | 65.77 | 1309 |
| HSA-MIR-3915 | 99.45 | 68.49 | 1905 |
| HSA-MIR-519D-5P | 99.41 | 69.30 | 2057 |
| HSA-MIR-185-5P | 99.35 | 68.60 | 2497 |
| HSA-MIR-4644 | 99.35 | 69.12 | 2514 |
| HSA-MIR-6731-5P | 99.28 | 67.42 | 2375 |
Literature-anchored findings (GeneRIF, showing 6)
- structural analysis of human pFGE by X-ray crystallography [pFGE] (PMID:15687489)
- pFGE (SUMF2) is the paralog of the Calpha-formylglycine-generating enzyme (PMID:15708861)
- SUMF2 interacts with sulphatase-modifying factor 1 to regulate sulphatase activities. (PMID:15962010)
- pFGE is retained in the ER through its C-terminal tetrapeptide PGEL, a noncanonical variant of the classic KDEL ER-retention signal. (PMID:18266766)
- SUMF2 interacted with IL-13 and inhibited IL-13 secretion in bronchial smooth muscle cells and lymphocytes, which was independent of IL-13 glycosylation (PMID:19739097)
- Differential DNA methylation analysis of SUMF2, ADAMTS5, and PXDN provides novel insights into colorectal cancer prognosis prediction in Taiwan. (PMID:35317099)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | sumf2 | ENSDARG00000069497 |
| mus_musculus | Sumf2 | ENSMUSG00000025538 |
| rattus_norvegicus | Sumf2 | ENSRNOG00000000922 |
Paralogs (1): SUMF1 (ENSG00000144455)
Protein
Protein identifiers
Inactive C-alpha-formylglycine-generating enzyme 2 — Q8NBJ7 (reviewed: Q8NBJ7)
Alternative names: Paralog of formylglycine-generating enzyme, Sulfatase-modifying factor 2
All UniProt accessions (15): Q8NBJ7, A0A494C1B1, A8MXB9, C9J660, C9JL30, E9PBT8, E9PG02, F8WA42, F8WCW9, F8WES7, F8WEV7, F8WEX5, H7C3B2, J3KQJ1, J3QT17
UniProt curated annotations — full annotation on UniProt →
Function. Lacks formylglycine generating activity and is unable to convert newly synthesized inactive sulfatases to their active form. Inhibits the activation of sulfatases by SUMF1.
Subunit / interactions. Homodimer and heterodimer with SUMF1.
Subcellular location. Endoplasmic reticulum lumen.
Tissue specificity. Detected in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Highest levels in kidney, liver and placenta.
Domain organisation. The non-canonical ER retention motif mediates retention of the protein in the endoplasmic reticulum.
Similarity. Belongs to the sulfatase-modifying factor family.
Isoforms (5)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q8NBJ7-1 | 1 | yes |
| Q8NBJ7-2 | 2 | |
| Q8NBJ7-3 | 3 | |
| Q8NBJ7-5 | 5 | |
| Q8NBJ7-4 | 4 |
RefSeq proteins (9): NP_001035933, NP_001035934, NP_001035935, NP_001123541, NP_001139805, NP_001353576, NP_001353577, NP_001353578, NP_056226* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR005532 | SUMF_dom | Domain |
| IPR016187 | CTDL_fold | Homologous_superfamily |
| IPR042095 | SUMF_sf | Homologous_superfamily |
| IPR051043 | Sulfatase_Mod_Factor_Kinase | Family |
Pfam: PF03781
UniProt features (46 total): strand 12, binding site 8, helix 7, mutagenesis site 5, splice variant 4, sequence variant 2, signal peptide 1, chain 1, glycosylation site 1, disulfide bond 1, region of interest 1, short sequence motif 1, turn 1, compositionally biased region 1
Structure
Experimental structures (PDB)
1 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 1Y4J | X-RAY DIFFRACTION | 1.86 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8NBJ7-F1 | 91.37 | 0.85 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Ligand- & substrate-binding residues (8): 232; 234; 236; 194; 195; 208; 210; 229
Disulfide bonds (1): 156–290
Glycosylation sites (1): 191
Mutagenesis-validated functional residues (5):
| Position | Phenotype |
|---|---|
| 156 | abolishes interaction with and inhibition of sumf1. can still form homodimers. |
| 290 | abolishes interaction with and inhibition of sumf1. can still form homodimers. |
| 298–301 | abolishes endoplasmic reticulum retention. |
| 298–299 | does not affect endoplasmic reticulum retention. |
| 298 | does not affect endoplasmic reticulum retention. |
Function
Pathways and Gene Ontology
Reactome pathways
9 pathways
| ID | Pathway |
|---|---|
| R-HSA-1663150 | The activation of arylsulfatases |
| R-HSA-9840310 | Glycosphingolipid catabolism |
| R-HSA-1430728 | Metabolism |
| R-HSA-163841 | Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation |
| R-HSA-1660662 | Glycosphingolipid metabolism |
| R-HSA-392499 | Metabolism of proteins |
| R-HSA-428157 | Sphingolipid metabolism |
| R-HSA-556833 | Metabolism of lipids |
| R-HSA-597592 | Post-translational protein modification |
MSigDB gene sets: 79 (showing top):
GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, REACTOME_SPHINGOLIPID_METABOLISM, GCM_NF2, ACEVEDO_LIVER_CANCER_UP, GOCC_ENDOPLASMIC_RETICULUM_LUMEN, YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, GCM_DENR, REACTOME_GAMMA_CARBOXYLATION_HYPUSINYLATION_HYDROXYLATION_AND_ARYLSULFATASE_ACTIVATION, REACTOME_METABOLISM_OF_LIPIDS, ATF6_TARGET_GENES, DLX2_TARGET_GENES
GO Biological Process (0):
GO Molecular Function (3): identical protein binding (GO:0042802), metal ion binding (GO:0046872), protein binding (GO:0005515)
GO Cellular Component (2): endoplasmic reticulum (GO:0005783), endoplasmic reticulum lumen (GO:0005788)
Reactome top-level categories
Rollup of top-7 pathways:
| Category | Pathways |
|---|---|
| Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation | 1 |
| Glycosphingolipid metabolism | 1 |
| Post-translational protein modification | 1 |
| Sphingolipid metabolism | 1 |
| Metabolism of lipids | 1 |
| Metabolism | 1 |
| Metabolism of proteins | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| protein binding | 1 |
| cation binding | 1 |
| binding | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| endoplasmic reticulum | 1 |
| intracellular organelle lumen | 1 |
Protein interactions and networks
STRING
1141 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SUMF2 | ZNF713 | Q8N859 | 651 |
| SUMF2 | PHKG1 | Q16816 | 642 |
| SUMF2 | CCT6A | P40227 | 600 |
| SUMF2 | NIPSNAP2 | O75323 | 562 |
| SUMF2 | CHCHD2 | Q9Y6H1 | 519 |
| SUMF2 | ERP44 | Q9BS26 | 498 |
| SUMF2 | LMAN1 | P49257 | 495 |
| SUMF2 | SUMF1 | Q8NBK3 | 489 |
| SUMF2 | PSPH | P78330 | 467 |
| SUMF2 | MXRA7 | P84157 | 463 |
| SUMF2 | FOXRED2 | Q8IWF2 | 452 |
| SUMF2 | ATRAID | Q6UW56 | 450 |
| SUMF2 | SEPTIN14 | Q6ZU15 | 445 |
| SUMF2 | TMEM161B | Q8NDZ6 | 443 |
| SUMF2 | NUPR2 | A6NF83 | 442 |
IntAct
69 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SUMF1 | SGSH | psi-mi:“MI:0914”(association) | 0.710 |
| SUMF2 | psi-mi:“MI:0915”(physical association) | 0.660 | |
| SUMF1 | SUMF2 | psi-mi:“MI:0915”(physical association) | 0.640 |
| SUMF2 | SUMF1 | psi-mi:“MI:0915”(physical association) | 0.640 |
| SUMF1 | SUMF2 | psi-mi:“MI:0403”(colocalization) | 0.640 |
| SUMF2 | APBB2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SUMF2 | CTSD | psi-mi:“MI:0915”(physical association) | 0.560 |
| SUMF2 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| GRN | SUMF2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SUMF2 | HSPB1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SUMF2 | PMP22 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SUMF2 | TTR | psi-mi:“MI:0915”(physical association) | 0.560 |
| SUMF2 | WFS1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SUMF2 | KIF1B | psi-mi:“MI:0915”(physical association) | 0.560 |
| HTT | SUMF2 | psi-mi:“MI:0915”(physical association) | 0.560 |
BioGRID (78): SUMF2 (Two-hybrid), ANKRD40 (Affinity Capture-MS), APOD (Affinity Capture-MS), CLU (Affinity Capture-MS), WDR34 (Affinity Capture-MS), APOD (Affinity Capture-MS), ANKRD40 (Affinity Capture-MS), SUMF2 (Affinity Capture-MS), SUMF2 (Co-fractionation), SUMF2 (Co-fractionation), SUMF2 (Co-fractionation), GRHPR (Co-fractionation), SUMF2 (Co-fractionation), SUMF2 (Co-fractionation), ABHD11 (Co-fractionation)
ESM2 similar proteins: A0R5N0, A0R6E0, D1A7C3, G7CFI3, I6Y8I5, O69671, P0A4Y5, P0A5F6, P16954, P28604, P45798, P71741, P9WIQ8, P9WIQ9, P9WQ18, P9WQ19, P9WQ24, P9WQ25, Q0AA26, Q0BU54, Q11EX1, Q1D654, Q1QJC0, Q210H1, Q216J6, Q28MN2, Q2IYX0, Q2J6Q9, Q2RR72, Q2W2Q6, Q2YB47, Q3AYE2, Q3SMH1, Q46TF2, Q47SE7, Q58CP2, Q59832, Q5N4W5, Q5NXV7, Q5RCR5
Diamond homologs: A0A0H3MBJ2, D1A7C3, O69671, P0DPS7, Q0P5L5, Q58CP2, Q5RCR5, Q7AJA5, Q7D513, Q822R1, Q8NBJ7, Q8R0F3, Q9F3C7, Q9PKP3, A0R5N0, G7CFI3, Q8BPG6, Q8NBK3, I6Y8I5, V9TSX0, Q7RX33, O94632, O34722
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
123 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 86 |
| Likely benign | 11 |
| Benign | 3 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 2678 | NM_015411.4(SUMF2):c.536-2del | Pathogenic |
SpliceAI
1515 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 7:56064374:GCTAG:G | donor_gain | 1.0000 |
| 7:56064375:C:G | donor_gain | 1.0000 |
| 7:56064377:AGG:A | donor_loss | 1.0000 |
| 7:56064378:GGT:G | donor_loss | 1.0000 |
| 7:56068478:GCA:G | acceptor_loss | 1.0000 |
| 7:56068479:CAG:C | acceptor_loss | 1.0000 |
| 7:56068480:AG:A | acceptor_gain | 1.0000 |
| 7:56068481:G:A | acceptor_loss | 1.0000 |
| 7:56068481:GG:G | acceptor_gain | 1.0000 |
| 7:56068481:GGA:G | acceptor_gain | 1.0000 |
| 7:56068481:GGAA:G | acceptor_gain | 1.0000 |
| 7:56074748:A:G | donor_gain | 1.0000 |
| 7:56076787:A:AG | acceptor_gain | 1.0000 |
| 7:56078097:A:AG | acceptor_gain | 1.0000 |
| 7:56078097:ATCAG:A | acceptor_gain | 1.0000 |
| 7:56078100:A:AG | acceptor_gain | 1.0000 |
| 7:56078100:AG:A | acceptor_gain | 1.0000 |
| 7:56078100:AGG:A | acceptor_gain | 1.0000 |
| 7:56078101:G:GA | acceptor_gain | 1.0000 |
| 7:56078101:GG:G | acceptor_gain | 1.0000 |
| 7:56078101:GGG:G | acceptor_gain | 1.0000 |
| 7:56078101:GGGA:G | acceptor_gain | 1.0000 |
| 7:56078101:GGGAA:G | acceptor_gain | 1.0000 |
| 7:56078184:ACGGT:A | donor_loss | 1.0000 |
| 7:56078185:CGGT:C | donor_loss | 1.0000 |
| 7:56078186:GGT:G | donor_loss | 1.0000 |
| 7:56078187:G:GG | donor_gain | 1.0000 |
| 7:56078187:GTA:G | donor_loss | 1.0000 |
| 7:56078188:T:C | donor_loss | 1.0000 |
| 7:56064379:G:GG | donor_gain | 0.9900 |
AlphaMissense
1954 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 7:56078396:T:A | W237R | 0.996 |
| 7:56078396:T:C | W237R | 0.996 |
| 7:56074210:T:A | W126R | 0.995 |
| 7:56074210:T:C | W126R | 0.995 |
| 7:56073049:A:C | S93R | 0.994 |
| 7:56073051:C:A | S93R | 0.994 |
| 7:56073051:C:G | S93R | 0.994 |
| 7:56074212:G:C | W126C | 0.994 |
| 7:56074212:G:T | W126C | 0.994 |
| 7:56074643:A:C | S148R | 0.993 |
| 7:56074645:C:A | S148R | 0.993 |
| 7:56074645:C:G | S148R | 0.993 |
| 7:56074669:T:G | C156W | 0.993 |
| 7:56078398:G:C | W237C | 0.993 |
| 7:56078398:G:T | W237C | 0.993 |
| 7:56079569:T:C | F288S | 0.993 |
| 7:56074708:G:C | W169C | 0.992 |
| 7:56074708:G:T | W169C | 0.992 |
| 7:56074706:T:A | W169R | 0.991 |
| 7:56074706:T:C | W169R | 0.991 |
| 7:56078386:C:A | N233K | 0.991 |
| 7:56078386:C:G | N233K | 0.991 |
| 7:56078392:G:C | W235C | 0.991 |
| 7:56078392:G:T | W235C | 0.991 |
| 7:56074716:C:A | A172D | 0.990 |
| 7:56076850:G:C | W184C | 0.990 |
| 7:56076850:G:T | W184C | 0.990 |
| 7:56078454:C:T | S256F | 0.990 |
| 7:56068635:T:C | F74S | 0.989 |
| 7:56074668:G:A | C156Y | 0.989 |
dbSNP variants (sampled 300 via entrez): RS1000370165 (7:56073776 C>T), RS1000385302 (7:56081391 G>A), RS1000650644 (7:56079652 A>G), RS1000681720 (7:56079853 A>G), RS1000705531 (7:56075433 A>G), RS1000759113 (7:56075652 T>C,G), RS1000776892 (7:56080079 C>T), RS1000831888 (7:56085417 G>A), RS1000925152 (7:56063059 G>A), RS1000956411 (7:56088151 C>T), RS1000975607 (7:56063258 T>A), RS1001668431 (7:56080770 T>A), RS1001689290 (7:56088315 C>A), RS1001764386 (7:56086164 T>A), RS1001987926 (7:56073458 A>G)
Disease associations
OMIM: gene MIM:607940 | disease phenotypes: MIM:272200
GenCC curated gene-disease
Mondo (1): mucosulfatidosis (MONDO:0010088)
Orphanet (1): Multiple sulfatase deficiency (Orphanet:585)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
4 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST007382_32 | Plasma free amino acid levels (adjusted for twenty other PFAAs) | 1.000000e-25 |
| GCST007385_29 | Plasma free amino acid levels | 2.000000e-21 |
| GCST012251_16 | Macular telangiectasia type 2 | 3.000000e-07 |
| GCST012252_7 | Macular telangiectasia type 2 | 6.000000e-09 |
EFO canonical traits (3, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0005134 | amino acid measurement |
| EFO:0009774 | serine measurement |
| EFO:1002009 | macular telangiectasia type 2 |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D052517 | Multiple Sulfatase Deficiency Disease | C10.228.140.163.100.435.825.850.750; C16.320.565.189.435.825.850.750; C16.320.565.398.641.803.925.750; C16.320.565.595.554.825.850.750; C18.452.132.100.435.825.850.750; C18.452.584.563.641.803.925.750; C18.452.648.189.435.825.850.750; C18.452.648.398.641.803.925.750; C18.452.648.595.554.825.850.750 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
39 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| bisphenol A | decreases expression, increases expression | 2 |
| sodium arsenite | decreases expression, increases abundance | 2 |
| Benzo(a)pyrene | affects methylation, increases methylation | 2 |
| Cisplatin | affects expression, affects cotreatment, increases expression | 2 |
| Ozone | affects expression, increases abundance, affects cotreatment, increases oxidation | 2 |
| Valproic Acid | increases expression | 2 |
| aristolochic acid I | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| beta-lapachone | increases expression | 1 |
| arsenite | affects binding, increases reaction | 1 |
| tetrabromobisphenol A | decreases expression | 1 |
| methacrylaldehyde | increases oxidation, affects cotreatment | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| calfactant | affects cotreatment, increases expression | 1 |
| K 7174 | increases expression | 1 |
| ICG 001 | increases expression | 1 |
| bisphenol B | increases expression | 1 |
| 2,2’,4,4’-tetrabromodiphenyl ether | decreases expression | 1 |
| hexabrominated diphenyl ether 153 | decreases expression | 1 |
| jinfukang | affects cotreatment, increases expression | 1 |
| bisphenol AF | increases expression | 1 |
| Resveratrol | affects cotreatment, increases expression | 1 |
| Decitabine | affects expression | 1 |
| Acrolein | affects cotreatment, increases oxidation | 1 |
| Air Pollutants | affects expression, increases abundance | 1 |
| Arsenic | decreases expression, increases abundance | 1 |
| Doxorubicin | decreases expression | 1 |
| Gallic Acid | decreases expression | 1 |
| Ivermectin | decreases expression | 1 |
| Plant Extracts | increases expression, affects cotreatment | 1 |
Clinical trials (associated diseases)
6 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT01841983 | Not specified | COMPLETED | Project A: Integrated Approaches to Improving the Health and Safety of Health Care Workers |
| NCT02699190 | Not specified | COMPLETED | LeukoSEQ: Whole Genome Sequencing as a First-Line Diagnostic Tool for Leukodystrophies |
| NCT03047369 | Not specified | RECRUITING | The Myelin Disorders Biorepository Project |
| NCT03333200 | Not specified | RECRUITING | Longitudinal Study of Neurodegenerative Disorders |
| NCT03831737 | Not specified | COMPLETED | Team-based Ergonomics Educational Model for Workplace WELLNESS Improvement: A Pilot Study |
| NCT06036693 | Not specified | RECRUITING | MPS (RaDiCo Cohort) (RaDiCo-MPS) |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): mucosulfatidosis