ERICH2
gene geneOn this page
Summary
ERICH2 (glutamate rich 2, HGNC:44395) is a protein-coding gene on chromosome 2q31.1, encoding Glutamate-rich protein 2 (A1L162).
At a glance
- GWAS associations: 2
- Clinical variants (ClinVar): 2 total — 1 pathogenic
- GTEx eGene: eQTL in 26 tissues, sQTL in 2 (q < 0.05)
- Constraint (gnomAD): pLI 0.10 (intermediate), LOEUF 1.54 (unconstrained)
- MANE Select transcript:
NM_001290030
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:44395 |
| Approved symbol | ERICH2 |
| Name | glutamate rich 2 |
| Location | 2q31.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000204334 |
| Ensembl biotype | protein_coding |
| OMIM | 620858 |
| Entrez | 285141 |
Gene structure
Transcript identifiers
Ensembl transcripts: 23 — 11 protein_coding, 6 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 2 retained_intron
MANE Select: ENST00000697325
Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 3: 2
ENST00000697325, ENST00000409885, ENST00000426475, ENST00000429172, ENST00000653024, ENST00000654532, ENST00000661942, ENST00000662201, ENST00000662915, ENST00000663589, ENST00000663834, ENST00000664870, ENST00000669009, ENST00000670985, ENST00000671618, ENST00000688829, ENST00000689478, ENST00000697326, ENST00000697327, ENST00000697344, ENST00001128508, ENST00001128509, ENST00001128510
RefSeq mRNA: 8 — MANE Select: NM_001290030
NM_001289947, NM_001290030, NM_001290031, NM_001388467, NM_001388468, NM_001388469, NM_001388470, NM_001388471
CCDS: CCDS77486, CCDS92894, CCDS92895
Canonical transcript exons
ENST00000697325 — 10 exons
| Exon | Start | End |
|---|---|---|
| ENSE00003970273 | 170792863 | 170792920 |
| ENSE00003970274 | 170777377 | 170777425 |
| ENSE00003970275 | 170798770 | 170798977 |
| ENSE00003970276 | 170779793 | 170779888 |
| ENSE00003970277 | 170770378 | 170771187 |
| ENSE00003970278 | 170798041 | 170798112 |
| ENSE00003970279 | 170782241 | 170782389 |
| ENSE00003970280 | 170784646 | 170784833 |
| ENSE00003970281 | 170777644 | 170777680 |
| ENSE00003970282 | 170777147 | 170777177 |
Expression profiles
Bgee: expression breadth ubiquitous, 127 present calls, max score 98.44.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.9468 / max 153.3689, expressed in 1170 samples.
Highest expression (Bgee): testis, male germ line stem cell (sensu Vertebrata) in testis, olfactory segment of nasal mucosa, endometrium, hypothalamus.
Genetic regulation across tissues (GTEx eQTL / sQTL)
ERICH2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 26 tissues and its splicing (sQTL) in 2 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.
showing 20 of 28 significant tissue × QTL associations:
| Tissue | QTL | q-value | Slope | Lead variant |
|---|---|---|---|---|
| Testis | sqtl | 1.8e-60 | -1.35 | 2:170785591:GTTAT:G |
| Artery Tibial | eqtl | 1.4e-21 | +0.40 | 2:170377725:C:G |
| Artery Aorta | eqtl | 5.0e-08 | +0.41 | 2:170377725:C:G |
| Testis | eqtl | 8.3e-07 | +0.10 | 2:170753131:C:A |
| Heart Atrial Appendage | eqtl | 2.2e-06 | -0.28 | 2:170716430:G:A |
| Artery Coronary | eqtl | 3.2e-05 | +0.44 | 2:170377725:C:G |
| Brain Hypothalamus | eqtl | 8.6e-05 | -0.38 | 2:170786963:G:C |
| Nerve Tibial | eqtl | 2.4e-04 | +0.22 | 2:170754390:T:TA |
| Brain Cerebellar Hemisphere | eqtl | 3.2e-04 | +0.53 | 2:170786382:G:A |
| Cells Cultured fibroblasts | eqtl | 5.6e-04 | -0.17 | 2:170785846:A:G |
| Pancreas | eqtl | 6.4e-04 | -0.34 | 2:170795855:G:A |
| Esophagus Mucosa | eqtl | 1.4e-03 | +0.42 | 2:170423868:C:T |
| Brain Cortex | eqtl | 1.8e-03 | +0.36 | 2:170774748:G:T |
| Brain Caudate basal ganglia | eqtl | 1.8e-03 | -0.32 | 2:170801872:T:C |
| Stomach | eqtl | 2.5e-03 | -0.20 | 2:170787540:A:G |
| Brain Anterior cingulate cortex BA24 | eqtl | 2.9e-03 | -0.35 | 2:170804976:G:A |
| Heart Left Ventricle | eqtl | 3.0e-03 | -0.27 | 2:170787540:A:G |
| Brain Spinal cord cervical c-1 | eqtl | 4.2e-03 | -0.35 | 2:170787540:A:G |
| Thyroid | eqtl | 7.0e-03 | -0.21 | 2:170740497:G:C |
| Esophagus Muscularis | eqtl | 9.8e-03 | -0.24 | 2:170787540:A:G |
FANTOM5 promoters
showing 10 of 11 alternative TSS:
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 23624 | 4.6887 | 1046 |
| 23623 | 1.2914 | 635 |
| 23625 | 0.3704 | 188 |
| 23622 | 0.2532 | 143 |
| 23620 | 0.1375 | 43 |
| 23621 | 0.1312 | 61 |
| 23627 | 0.0491 | 3 |
| 23618 | 0.0107 | 4 |
| 23626 | 0.0056 | 3 |
| 23619 | 0.0055 | 2 |
Top tissues by expression
showing 100 of 134 tissues by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| left testis | UBERON:0004533 | 98.44 | gold quality |
| testis | UBERON:0000473 | 98.05 | gold quality |
| right testis | UBERON:0004534 | 98.01 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 92.24 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 87.39 | gold quality |
| endometrium | UBERON:0001295 | 78.18 | gold quality |
| hypothalamus | UBERON:0001898 | 78.07 | gold quality |
| right uterine tube | UBERON:0001302 | 77.80 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 77.69 | gold quality |
| right lung | UBERON:0002167 | 76.74 | gold quality |
| amygdala | UBERON:0001876 | 76.27 | gold quality |
| temporal lobe | UBERON:0001871 | 76.12 | gold quality |
| lung | UBERON:0002048 | 76.08 | gold quality |
| substantia nigra | UBERON:0002038 | 75.27 | gold quality |
| nucleus accumbens | UBERON:0001882 | 75.21 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 75.17 | gold quality |
| islet of Langerhans | UBERON:0000006 | 74.69 | gold quality |
| body of pancreas | UBERON:0001150 | 74.26 | gold quality |
| fallopian tube | UBERON:0003889 | 74.02 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 74.02 | gold quality |
| Ammon’s horn | UBERON:0001954 | 73.40 | gold quality |
| body of stomach | UBERON:0001161 | 73.33 | gold quality |
| pancreas | UBERON:0001264 | 73.15 | gold quality |
| caudate nucleus | UBERON:0001873 | 72.96 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 72.91 | gold quality |
| putamen | UBERON:0001874 | 72.85 | gold quality |
| endocervix | UBERON:0000458 | 72.62 | gold quality |
| tibial artery | UBERON:0007610 | 72.61 | gold quality |
| popliteal artery | UBERON:0002250 | 72.60 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 72.17 | gold quality |
| cerebral cortex | UBERON:0000956 | 72.07 | gold quality |
| prefrontal cortex | UBERON:0000451 | 71.69 | gold quality |
| frontal cortex | UBERON:0001870 | 71.63 | gold quality |
| right frontal lobe | UBERON:0002810 | 71.44 | gold quality |
| right atrium auricular region | UBERON:0006631 | 71.37 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 71.32 | gold quality |
| brain | UBERON:0000955 | 71.22 | gold quality |
| fundus of stomach | UBERON:0001160 | 71.16 | gold quality |
| right lobe of liver | UBERON:0001114 | 71.12 | gold quality |
| apex of heart | UBERON:0002098 | 70.89 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 69.84 | gold quality |
| primary visual cortex | UBERON:0002436 | 69.75 | gold quality |
| stomach | UBERON:0000945 | 69.72 | gold quality |
| left coronary artery | UBERON:0001626 | 68.84 | gold quality |
| body of uterus | UBERON:0009853 | 68.18 | gold quality |
| saliva-secreting gland | UBERON:0001044 | 68.14 | gold quality |
| mucosa of stomach | UBERON:0001199 | 68.08 | gold quality |
| minor salivary gland | UBERON:0001830 | 68.05 | gold quality |
| subcutaneous adipose tissue | UBERON:0002190 | 67.97 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 67.94 | gold quality |
| heart | UBERON:0000948 | 67.84 | gold quality |
| uterine cervix | UBERON:0000002 | 67.69 | gold quality |
| heart left ventricle | UBERON:0002084 | 67.69 | gold quality |
| adipose tissue | UBERON:0001013 | 67.54 | gold quality |
| ectocervix | UBERON:0012249 | 67.04 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 67.02 | gold quality |
| adenohypophysis | UBERON:0002196 | 66.95 | gold quality |
| omental fat pad | UBERON:0010414 | 66.95 | gold quality |
| myometrium | UBERON:0001296 | 66.85 | gold quality |
| left uterine tube | UBERON:0001303 | 66.84 | gold quality |
| thoracic mammary gland | UBERON:0005200 | 66.35 | gold quality |
| right adrenal gland | UBERON:0001233 | 66.34 | gold quality |
| thoracic aorta | UBERON:0001515 | 66.25 | gold quality |
| ascending aorta | UBERON:0001496 | 66.16 | gold quality |
| pituitary gland | UBERON:0000007 | 66.11 | gold quality |
| liver | UBERON:0002107 | 66.08 | gold quality |
| left adrenal gland | UBERON:0001234 | 66.02 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 66.01 | gold quality |
| lower esophagus | UBERON:0013473 | 65.97 | gold quality |
| calcaneal tendon | UBERON:0003701 | 65.90 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 65.81 | gold quality |
| metanephros cortex | UBERON:0010533 | 65.26 | gold quality |
| cerebellum | UBERON:0002037 | 65.23 | gold quality |
| cerebellar cortex | UBERON:0002129 | 65.20 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 65.15 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 64.92 | gold quality |
| adult mammalian kidney | UBERON:0000082 | 64.80 | gold quality |
| gall bladder | UBERON:0002110 | 64.78 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 64.62 | gold quality |
| tibial nerve | UBERON:0001323 | 64.39 | gold quality |
| cortex of kidney | UBERON:0001225 | 64.29 | gold quality |
| urinary bladder | UBERON:0001255 | 63.77 | gold quality |
| multicellular organism | UBERON:0000468 | 63.50 | gold quality |
| prostate gland | UBERON:0002367 | 63.37 | gold quality |
| adrenal gland | UBERON:0002369 | 63.30 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 62.96 | gold quality |
| gastrocnemius | UBERON:0001388 | 62.83 | gold quality |
| right coronary artery | UBERON:0001625 | 62.83 | gold quality |
| ovary | UBERON:0000992 | 62.70 | gold quality |
| corpus callosum | UBERON:0002336 | 62.36 | gold quality |
| muscle of leg | UBERON:0001383 | 62.14 | gold quality |
| left ovary | UBERON:0002119 | 62.06 | gold quality |
| kidney | UBERON:0002113 | 62.04 | gold quality |
| right ovary | UBERON:0002118 | 61.71 | gold quality |
| thyroid gland | UBERON:0002046 | 61.58 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 61.48 | gold quality |
| vagina | UBERON:0000996 | 61.36 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 60.77 | gold quality |
| esophagus | UBERON:0001043 | 59.94 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 59.87 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 12.38 |
HPA expression
RNA tissue specificity: Group enriched
showing 60 of 75 HPA tissues / cells by nTPM:
| Tissue / cell | Axis | nTPM |
|---|---|---|
| Testis | tissue | 100.8 |
| Olfactory bulb | tissue | 33.6 |
| Choroid plexus | tissue | 28.5 |
| Basal ganglia | tissue | 12.0 |
| Thyroid gland | tissue | 10.0 |
| Nucleus accumbens | tissue | 9.7 |
| Septum | tissue | 9.3 |
| Lung | tissue | 9.1 |
| Periaqueductal gray | tissue | 8.1 |
| Cerebellum | tissue | 7.8 |
| Ventral forebrain | tissue | 7.2 |
| Putamen | tissue | 6.6 |
| Fallopian tube | tissue | 6.3 |
| Parathyroid gland | tissue | 6.2 |
| Hippocampus | tissue | 5.7 |
| Retina | tissue | 5.2 |
| Locus coeruleus | tissue | 5.0 |
| Thalamus | tissue | 4.9 |
| Hippocampal formation | tissue | 4.8 |
| Hypothalamus | tissue | 4.4 |
| Postcentral gyrus | tissue | 4.4 |
| Pancreas | tissue | 3.8 |
| Amygdala | tissue | 3.7 |
| Kidney | tissue | 3.5 |
| Epididymis | tissue | 3.4 |
| Cervix | tissue | 3.2 |
| Superior colliculi | tissue | 3.2 |
| Liver | tissue | 3.2 |
| Endometrium 1 | tissue | 3.1 |
| Stomach 1 | tissue | 2.7 |
| Pons | tissue | 2.7 |
| Heart muscle | tissue | 2.6 |
| Salivary gland | tissue | 2.5 |
| Cerebral cortex | tissue | 2.3 |
| Tongue | tissue | 2.3 |
| Retrosplenial and cingulate cortex | tissue | 2.3 |
| Medulla oblongata | tissue | 2.2 |
| Insular cortex | tissue | 2.2 |
| Adrenal gland | tissue | 2.1 |
| Entorhinal cortex | tissue | 2.1 |
| Breast | tissue | 2.0 |
| Seminal vesicle | tissue | 1.9 |
| Prostate | tissue | 1.9 |
| Retrosplenial cortex | tissue | 1.9 |
| Temporal cortex | tissue | 1.9 |
| Prefrontal cortex | tissue | 1.8 |
| Motor cortex | tissue | 1.8 |
| Occipital cortex | tissue | 1.8 |
| Midbrain | tissue | 1.5 |
| Somatosensory cortex | tissue | 1.4 |
| Pituitary gland | tissue | 1.3 |
| Ovary | tissue | 1.3 |
| Corpus callosum | tissue | 1.3 |
| Caudate putamen | tissue | 1.2 |
| Adipose tissue | tissue | 1.1 |
| Vagina | tissue | 0.9 |
| Skeletal muscle | tissue | 0.8 |
| Substantia nigra | tissue | 0.8 |
| Duodenum | tissue | 0.8 |
| Spinal cord | tissue | 0.8 |
Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Arcuate nucleus (12.1), Posterior thalamic nucleus (10.3), Preoptic area (10.2), Dorsomedial nucleus (9.4), Caudate nucleus (9.2).
Regulation
Is transcription factor: no
Functional genomics
gnomAD constraint: pLI 0.104, LOEUF 1.54, missense Z 0.106 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD
Regional missense constraint (gnomAD RMC): no regional variation along ENST00000409885 — one region, missense o/e 1.01.
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | erich2 | ENSDARG00000107534 |
| mus_musculus | Erich2 | ENSMUSG00000075302 |
| rattus_norvegicus | Erich2 | ENSRNOG00000056087 |
| drosophila_melanogaster | CG14853 | FBGN0038246 |
Mouse-model phenotypes
Observed phenotypes of the mouse ortholog (MGI:1913998) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 1 distinct phenotype terms.
| Mouse phenotype (MP) | Records |
|---|---|
| reproductive system phenotype | 1 |
Additional cross-species homologs
Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.
| Organism | UniProt | Identity | Method |
|---|---|---|---|
| Bos taurus | A6QQ66 | 76.1% | Diamond |
Genomic neighbors (locus context)
Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).
| Symbol | Type | Entrez |
|---|---|---|
| MYO3B-AS1 | ncRNA | 101929753 |
| GAD1-AS1 | ncRNA | 137805480 |
| MYO3B | protein-coding | 140469 |
| GAD1 | protein-coding | 2571 |
| GORASP2 | protein-coding | 26003 |
| SP5 | protein-coding | 389058 |
| LINC01124 | ncRNA | 440925 |
| ERICH2-DT | ncRNA | 101926913 |
| TLK1 | protein-coding | 9874 |
Protein
Protein identifiers
Glutamate-rich protein 2 — A1L162 (reviewed: A1L162)
All UniProt accessions (9): A0A8V8TKZ3, A0A8V8TLA6, A0A8V8TLB4, A0A8V8TLB8, A0A8V8TMA0, A0A8V8TMB5, A0A8V8TMI2, A0A8V8TMJ1, A1L162
UniProt curated annotations — full annotation on UniProt →
RefSeq proteins (8): NP_001276876, NP_001276959, NP_001276960, NP_001375396, NP_001375397, NP_001375398, NP_001375399, NP_001375400 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR026703 | ERICH2 | Family |
UniProt features (5 total): region of interest 2, compositionally biased region 2, chain 1
Structure
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-A1L162-F1 | 74.23 | 0.35 |
Human Protein Atlas
Protein class: Predicted intracellular proteins
Protein evidence: Evidence at protein level
Subcellular location (HPA, imaging): nucleoli fibrillar center; vesicles
Antibody reliability (HPA): IF approved
Function
Pathways and Gene Ontology
Reactome pathways
0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).
MSigDB gene sets: 31 (showing top):
GSE45365_NK_CELL_VS_CD8A_DC_DN, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, MIR153_5P, MIR12136, MIR335_3P, MIR4503, MIR548AV_5P_MIR548K, MIR8054, MIR302F, MIR2053, MIR20A_3P, MIR3168, MIR802, MIR3922_3P, GSE13306_TREG_VS_TCONV_SPLEEN_UP
GO Molecular Function (1): protein binding (GO:0005515)
GO top-level categories
1 GO namespaces:
| Category | Terms |
|---|---|
| binding | 1 |
Protein interactions and networks
STRING
showing 15 of 158 interactions by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| ERICH2 | PGBD2 | Q6P3X8 | 523 |
| ERICH2 | SH3RF3 | Q8TEJ3 | 506 |
| ERICH2 | PROSER1 | Q86XN7 | 439 |
| ERICH2 | GRAMD2A | Q8IUY3 | 438 |
| ERICH2 | CHAMP1 | Q96JM3 | 410 |
| ERICH2 | RHCE | P18577 | 384 |
| ERICH2 | TCF24 | Q7RTU0 | 374 |
| ERICH2 | ATAD1 | Q8NBU5 | 348 |
| ERICH2 | GPSM1 | Q86YR5 | 348 |
| ERICH2 | INSYN1 | Q2T9L4 | 347 |
| ERICH2 | PPP1R42 | Q7Z4L9 | 346 |
| ERICH2 | TRIM40 | Q6P9F5 | 335 |
| ERICH2 | SBK2 | P0C263 | 322 |
| ERICH2 | PDPR | Q8NCN5 | 318 |
| ERICH2 | H3BT10 | H3BT10 | 306 |
IntAct
Human interaction partners of ERICH2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).
6 partners by confidence:
| Partner | Interaction type | MIscore | Records |
|---|---|---|---|
| MACROH2A1 | physical association | 0.720 | 6 |
| HTT | physical association | 0.560 | 3 |
| IWS1 | physical association | 0.560 | 3 |
| PSORS1C2 | physical association | 0.560 | 3 |
| SDCBP | physical association | 0.560 | 3 |
| TNF | physical association | 0.000 | 1 |
BioGRID (6 interactions; top human partners by supporting records): H2AFY (Two-hybrid; 2 records), FBXO7 (Biochemical Activity), IWS1 (Two-hybrid), PSORS1C2 (Two-hybrid), SDCBP (Two-hybrid)
Disease & clinical
Genetic variants
Variant evidence for ERICH2: 2 ClinVar records (1 pathogenic / likely pathogenic); 2 GWAS associations. Per-variant detail is on Sugi Variant.
ClinVar
2 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 0 |
| Likely benign | 1 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (1)
Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.
| Variant ID | HGVS | Classification | Review | Submitters |
|---|---|---|---|---|
| 60252 | GRCh38/hg38 2q31.1(chr2:170101430-171243609)x1 | Pathogenic | criteria provided, single submitter | 1 |
Per-variant reference — Sugi Variant
Explore ERICH2’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.
SpliceAI
Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 23 predictions of 784):
| Position(s) | Effect | Δscore | Sites |
|---|---|---|---|
| 2:170784834–170784835 | donor_loss | 1.0000 | 3 |
| 2:170798762 | acceptor_gain | 1.0000 | |
| 2:170798765 | acceptor_gain | 1.0000 | |
| 2:170798769 | acceptor_loss | 1.0000 | 2 |
| 2:170782236 | acceptor_gain | 0.9900 | |
| 2:170782390–170782391 | donor_loss | 0.9900 | 6 |
| 2:170784644–170784645 | acceptor_loss | 0.9900 | 6 |
| 2:170784822 | donor_gain | 0.9900 | |
| 2:170784834 | donor_loss | 0.9900 | |
| 2:170792917 | donor_gain | 0.9900 |
AlphaMissense
223 missense substitutions predicted likely pathogenic (of 2,842 scored), across 48 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:
| Residue | Likely-pathogenic substitutions | Mean am_pathogenicity | Max am_pathogenicity |
|---|---|---|---|
| M78 | 9 | 0.888 | 0.970 |
| M91 | 9 | 0.877 | 0.987 |
| F73 | 8 | 0.976 | 0.999 |
| F105 | 8 | 0.942 | 0.998 |
| N99 | 8 | 0.883 | 0.982 |
| C89 | 7 | 0.975 | 0.996 |
| E96 | 7 | 0.957 | 0.987 |
| E72 | 7 | 0.943 | 0.976 |
| I92 | 7 | 0.896 | 0.993 |
| M70 | 7 | 0.868 | 0.969 |
| P66 | 6 | 0.986 | 0.995 |
| P97 | 6 | 0.935 | 0.966 |
| E68 | 6 | 0.922 | 0.974 |
| A102 | 6 | 0.914 | 0.995 |
| K87 | 6 | 0.888 | 0.930 |
| A65 | 6 | 0.827 | 0.993 |
| E77 | 6 | 0.776 | 0.975 |
| Y82 | 5 | 0.961 | 0.978 |
| A85 | 5 | 0.937 | 0.995 |
| Y95 | 5 | 0.934 | 0.988 |
HPA cancer prognostics
RNA cancer specificity: Low cancer specificity
Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.
3 prognostic cancer types:
| Cancer | Prognostic | p-value |
|---|---|---|
| Glioblastoma Multiforme (validation) | unfavorable | 2.51e-07 |
| Kidney Renal Papillary Cell Carcinoma (TCGA) | unfavorable | 0.00047 |
| Kidney Chromophobe (TCGA) | unfavorable | 0.000841 |
Disease associations
OMIM: gene MIM:620858 | disease phenotypes:
GWAS associations
2 associations:
| Study | Trait | p-value |
|---|---|---|
| GCST010244_197 | Triglyceride levels | 2e-11 |
| GCST009602_82 | Metabolic syndrome | 3e-8 |
EFO canonical traits (from GWAS)
2 canonical traits:
| EFO ID | Trait name |
|---|---|
| EFO:0000195 | metabolic syndrome |
| EFO:0004530 | triglyceride measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (CPIC guideline: no)
CTD chemical–gene interactions
14 total (human), top 14 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | decreases expression, increases expression | 2 |
| Air Pollutants | increases abundance, increases expression | 2 |
| titanium dioxide | decreases expression | 1 |
| methylparaben | increases expression | 1 |
| versicolorin A | increases expression | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects cotreatment, increases expression | 1 |
| perfluoro-n-nonanoic acid | increases expression | 1 |
| Vehicle Emissions | increases abundance, increases expression | 1 |
| Dexamethasone | decreases expression | 1 |
| Lipopolysaccharides | affects cotreatment, increases expression | 1 |
| Smoke | increases abundance, increases expression | 1 |
| Okadaic Acid | decreases expression | 1 |
| Acrylamide | increases expression | 1 |
| Particulate Matter | increases abundance, increases expression | 1 |
Clinical trials (associated diseases)
Via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.