Genes in panel
- ACD 4
- ACP5 5
- ADA 9
- ADA2 5
- ADAM17 7
- ADAR 4
- AGR2 3
- AICDA 7
- AIRE 6
- AK2 7
- ALPI 4
- ALPK1 2
- ANKZF1 3
- AP3B1 5
- ARPC1B 5
- ARPC5 3
- ATM 4
- ATP6AP1 4
- B2M 5
- BACH2 5
- BCL10 6
- BLM 4
- BLNK 7
- BLOC1S6 5
- BTK 8
- C17orf62 4
- C1QA 4
- C1QB 5
- C1QC 4
- C1R 4
- C1S 4
- C2 6
- C2orf69 3
- C3 4
- C4A 4
- C4B 4
- C5 4
- C6 4
- C7 4
- C8A 4
- C8B 4
- C9 4
- CARD11 5
- CARD14 5
- CARD9 4
- CARMIL2 6
- CASP8 5
- CBLB 3
- CCBE1 5
- CD19 6
- CD247 9
- CD27 6
- CD3D 8
- CD3E 8
- CD3G 5
- CD4 7
- CD40 5
- CD40LG 5
- CD46 4
- CD55 4
- CD59 4
- CD70 5
- CD79A 7
- CD79B 6
- CD81 5
- CDC42 3
- CDCA7 4
- CEBPE 5
- CFD 4
- CFH 4
- CFI 4
- CFP 4
- CHD7 4
- CIB1 3
- CIITA 6
- CLPB 5
- COL7A1 4
- COPA 6
- CORO1A 7
- CR2 6
- CREBBP 3
- CSF2RA 4
- CSF2RB 5
- CSF3R 6
- CTLA4 7
- CTPS1 5
- CTSC 4
- CXCR2 6
- CXCR4 6
- CYBA 4
- CYBB 5
- DBR1 3
- DCLRE1C 8
- DEF6 5
- DIAPH1 3
- DKC1 4
- DNAJC21 4
- DNASE1L3 7
- DNASE2 4
- DNMT3B 6
- DOCK11 3
- DOCK2 5
- DOCK8 7
- DUT 3
- EFL1 3
- ELANE 6
- ELF4 8
- EP300 3
- EPG5 6
- ERCC6L2 4
- EXTL3 6
- F12 4
- FADD 5
- FAS 5
- FASLG 6
- FAT4 5
- FCHO1 4
- FERMT1 2
- FERMT3 4
- FNIP1 2
- FOXN1 9
- FOXP3 5
- G6PC3 6
- G6PD 4
- GATA1 5
- GATA2 4
- GFI1 6
- GINS1 4
- GNAI2 3
- GUCY2C 5
- HAVCR2 4
- HAX1 8
- HELLS 4
- HMOX1 5
- HPS1 4
- HPS4 4
- HPS6 4
- HSPA1L 5
- HTRA2 5
- HYOU1 6
- ICOS 7
- IFIH1 4
- IFNAR2 5
- IFNGR1 4
- IFNGR2 4
- IGHM 6
- IGLL1 6
- IKBKB 8
- IKBKG 5
- IKZF1 6
- IKZF2 4
- IKZF3 2
- IL10 5
- IL10RA 5
- IL10RB 5
- IL12B 4
- IL12RB1 4
- IL17RA 5
- IL17RC 4
- IL1RN 6
- IL21R 5
- IL23R 5
- IL2RA 5
- IL2RB 4
- IL2RG 8
- IL36RN 6
- IL6R 6
- IL6ST 7
- IL7 2
- IL7R 8
- INO80 5
- IRAK4 4
- IRF2BP2 5
- IRF4 5
- IRF7 4
- IRF8 4
- ISG15 4
- ITCH 5
- ITGB2 4
- ITK 7
- ITPR3 2
- JAGN1 4
- JAK1 6
- JAK3 8
- KDM6A 5
- KMT2A 4
- KMT2D 5
- LACC1 3
- LAMTOR2 6
- LAT 6
- LCK 5
- LCP2 5
- LIG1 6
- LIG4 8
- LPIN2 6
- LRBA 6
- LYN 3
- LYST 6
- MAGT1 7
- MALT1 6
- MAP3K14 6
- MCM4 7
- MCTS1 3
- MECOM 3
- MEFV 6
- MOGS 5
- MPEG1 2
- MSN 5
- MTHFD1 6
- MVK 6
- MYD88 6
- MYO5B 8
- MYSM1 5
- NBN 5
- NCF1 5
- NCF2 5
- NCF4 6
- NCKAP1L 2
- NFAT5 6
- NFE2L2 4
- NFKB1 5
- NFKB2 7
- NFKBIA 6
- NHEJ1 10
- NHP2 5
- NLRC4 6
- NLRP1 10
- NLRP12 6
- NLRP3 6
- NOD2 7
- NPC1 3
- NSMCE3 4
- NUDCD3 2
- OAS1 5
- ORAI1 8
- OTULIN 8
- PARN 5
- PAX1 3
- PEPD 5
- PGM3 5
- PI4KA 2
- PIK3CD 10
- PIK3CG 3
- PIK3R1 8
- PLCG2 9
- PLG 3
- PNP 7
- POLA1 5
- POLD1 6
- POLE 6
- POMP 2
- PRF1 5
- PRIM1 3
- PRKCD 6
- PRKDC 5
- PSMB10 6
- PSMB8 6
- PSTPIP1 6
- PTCRA 3
- PTPN2 5
- PTPRC 8
- RAB27A 6
- RAC2 9
- RAG1 8
- RAG2 8
- RANBP2 4
- RASGRP1 6
- RBCK1 6
- RECQL4 4
- REL 5
- RELA 6
- RELB 6
- RFX5 6
- RFXANK 6
- RFXAP 6
- RIPK1 7
- RMRP 8
- RNASEH2A 5
- RNASEH2B 5
- RNASEH2C 5
- RNF168 5
- RNU7-1 3
- RORC 5
- RPSA 5
- RTEL1 5
- SAMD9 4
- SAMD9L 7
- SAMHD1 5
- SASH3 4
- SBDS 6
- SEC61A1 7
- SERPING1 5
- SGPL1 5
- SH2D1A 5
- SKIV2L 6
- SLC29A3 5
- SLC35C1 5
- SLC37A4 6
- SLC39A7 5
- SLC46A1 5
- SLC7A7 4
- SLCO2A1 2
- SMARCAL1 6
- SMARCD2 4
- SNORA31 4
- SOCS1 2
- SP110 5
- SPI1 5
- SPINK5 6
- SPPL2A 5
- SRP54 4
- STAT1 5
- STAT2 5
- STAT3 5
- STAT4 6
- STAT5B 10
- STAT6 5
- STIM1 6
- STK4 6
- STX11 5
- STXBP2 5
- STXBP3 4
- SYK 3
- TAP1 5
- TAP2 5
- TAZ 6
- TBK1 6
- TBX1 9
- TCF3 10
- TCN2 10
- TET2 5
- TFRC 7
- TGFB1 4
- TGFBR1 2
- TGFBR2 2
- TICAM1 5
- TLR3 5
- TLR7 4
- TLR8 5
- TMC6 5
- TMC8 5
- TMEM173 7
- TNFAIP3 5
- TNFRSF1A 6
- TNFRSF9 4
- TOP2B 4
- TPP2 5
- TRAC 5
- TRAF3 5
- TRAF3IP2 8
- TREX1 5
- TRIM22 4
- TRNT1 4
- TTC37 6
- TTC7A 5
- TYK2 5
- UNC13D 5
- UNC93B1 5
- UNG 5
- USB1 4
- USP18 7
- VPS13B 5
- VPS45 5
- WAS 8
- WDR1 7
- WIPF1 5
- XIAP 6
- ZAP70 7
- ZBTB24 5
- ZNF341 5
- ZNFX1 4
- ANGPT1 2
- AP1S3 5
- AP3D1 3
- ATAD3A 2
- BCL11B 4
- CARD8 2
- CASP10 7
- CD8A 4
- CFB 4
- CFTR 3
- CTC1 4
- DCLRE1B 8
- DPP9 2
- ERBIN 3
- FCGR3A 3
- FGL2 2
- FLT3LG 3
- FMNL2 2
- FOXI3 2
- FPR1 2
- GCC2 2
- GIMAP5 5
- GTF3A 2
- IFNAR1 2
- IGKC 2
- IL17F 3
- IL1R1 2
- IL21 4
- IL27RA 3
- IPO8 3
- IRF1 2
- IRF3 2
- IRF9 2
- ITGAV 1
- ITPKB 2
- IVNS1ABP 3
- KCNA5 2
- KRAS 2
- MAN2B2 4
- MBL2 2
- MKL1 4
- MPO 3
- NCSTN 2
- NOP10 4
- NRAS 5
- POLD3 2
- POLR3A 2
- POLR3C 2
- PSENEN 3
- PSMA3 5
- PSMB4 5
- PSMB9 5
- PTEN 5
- QSOX2 1
- RC3H1 3
- REXO2 2
- RHBDF2 2
- RHOH 4
- RNF31 6
- SCGN 2
- SENP7 1
- SLC30A2 1
- SLC39A4 3
- SLC9A3 3
- SRP72 2
- TAPBP 3
- TERC 3
- TERT 3
- TINF2 3
- TMEFF1 2
- TNFRSF11A 4
- TNFRSF13C 2
- ABI3 1
- ACTB 2
- AMFR 2
- APOL1 2
- ARHGAP42 2
- ARHGEF1 2
- ASXL1 2
- ATG4A 2
- BRCA1 0
- BRCA2 0
- C8G 2
- CARD10 2
- CD274 2
- CD28 2
- CFHR1 4
- CFHR2 2
- CFHR3 4
- CFHR4 4
- CFHR5 6
- CHUK 2
- CLCN7 2
- CNBP 4
- COLEC11 2
- COPG1 2
- CRACR2A 2
- CSF2 2
- CTNNBL1 3
- CXorf36 1
- EPCAM 2
- ERCC2 2
- ERCC3 2
- ERCC4 0
- EZR 2
- FAAP24 3
- FANCF 0
- FANCI 0
- FANCM 0
- FBF1 2
- FBRS 1
- FCGR1A 2
- FCGR2A 2
- FCGR2B 2
- FCGR3B 4
- FCGRT 2
- FCN3 4
- FOXM1 1
- FPR2 2
- FPR3 2
- GAD1 5
- GIMAP6 2
- GTF2H5 1
- HCK 2
- HS3ST6 2
- ICOSLG 4
- IFNG 2
- IGHG2 2
- IL12RB2 2
- IL17A 2
- IL18 2
- IL18BP 2
- IL22 2
- IL23A 2
- IL31RA 1
- IL37 2
- IL6 1
- IRAK1 2
- ITGAM 2
- LRRC32 2
- LRRC8A 5
- LSM11 2
- LYZ 2
- MAP1LC3B2 2
- MAPK8 2
- MASP1 2
- MASP2 4
- MCM10 2
- MED13L 1
- MICA 1
- MPI 2
- MR1 2
- MRE11 3
- MS4A1 3
- MSH6 3
- MTPAP 1
- MYOF 2
- NBAS 2
- NFKBID 3
- NOS2 2
- ODC1 1
- OSTM1 2
- PARP1 1
- PDCD1 2
- PLEKHM1 2
- PMS2 5
- POLD2 2
- POLE2 2
- POLR3F 2
- POU2AF1 2
- PSEN1 3
- PSMG2 2
- PTPN22 1
- RAD50 2
- RAP1B 2
- RELN 1
- RET 3
- RGS10 2
- RHOG 2
- RNU4ATAC 2
- SAMD3 1
- SART3 3
- SEMA3E 3
- SH3BP2 3
- SH3KBP1 2
- SIRT1 2
- SLC13A4 1
- SNX10 1
- STAT5A 3
- STN1 1
- TBX21 2
- TCIRG1 1
- THBD 3
- TIRAP 2
- TLN1 1
- TNFRSF13B 8
- TNFRSF4 3
- TNFSF11 1
- TNFSF12 2
- TNFSF13 1
- TNFSF9 2
- TNIP1 1
- TOM1 2
- TSPAN14 1
- TUBGCP3 1
- UBA1 5
- UNC119 3
- WRAP53 1
- ZC3HC1 1
- ZFP36 1
- ZNF34 1
- GTF3AP5 1
STRs in panel
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Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: SCGN Amber List (moderate evidence)
SCGN (secretagogin, EF-hand calcium binding protein)
EnsemblGeneIds (GRCh38): ENSG00000079689
EnsemblGeneIds (GRCh37): ENSG00000079689
OMIM: 609202, Gene2Phenotype
SCGN is in 1 panel
EnsemblGeneIds (GRCh38): ENSG00000079689
EnsemblGeneIds (GRCh37): ENSG00000079689
OMIM: 609202, Gene2Phenotype
SCGN is in 1 panel
2 reviews
Achchuthan Shanmugasundram (Genomics England Curator)
I don't know
As reviewed by Hannah Knight, PMID:31663849 reported three siblings with homozygous missense SCGN variant and with early-onset ulcerative colitis. Functional studies demonstrated that SCGN variant identified impacted the localisation of the SNARE complex partner, SNAP25, leading to impaired hormone release. In addition, SCGN knockout mouse model recapitulated impaired hormone release and susceptibility to DSS-induced colitis.
This gene has not yet been associated with relevant phenotypes either in OMIM or in Gene2Phenotype.Created: 14 Feb 2024, 7:35 p.m. | Last Modified: 14 Feb 2024, 7:35 p.m.
Panel Version: 4.182
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
ulcerative colitis, MONDO:0005101
Publications
Created: 14 Feb 2024, 7:35 p.m.
Last Modified: 14 Feb 2024, 7:35 p.m.
Panel version: 4.182
Last Modified: 14 Feb 2024, 7:35 p.m.
Panel version: 4.182
Hannah Knight (NIHR BioResource - University of Cambridge)
Red List (low evidence)
Not linked to a phenotype in OMIM.
PMID: 31663849 (2019) reported three siblings with early onset UC, all with a homozygous missense variant in SCGN (p.Arg77His). Parents were both heterozygous. Some functional work done
Sources: LiteratureCreated: 13 Feb 2024, 11:25 a.m.
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
?early-onset ulcerative colitis
Publications
- PMID: 31663849
Created: 13 Feb 2024, 11:25 a.m.
Panel version: 4.163
Panel version: 4.163
Details
- Mode of Inheritance
- BIALLELIC, autosomal or pseudoautosomal
- Sources
-
- Expert Review Amber
- Phenotypes
-
- ulcerative colitis, MONDO:0005101
- OMIM
- 609202
- Clinvar variants
- Variants in SCGN
- Penetrance
- None
- Publications
- Panels with this gene
History Filter Activity
14 Feb 2024, Gel status: 2
Entity classified by Genomics England curator
Achchuthan Shanmugasundram (Genomics England Curator)Gene: scgn has been classified as Amber List (Moderate Evidence).
14 Feb 2024, Gel status: 0
Set Phenotypes
Achchuthan Shanmugasundram (Genomics England Curator)Phenotypes for gene: SCGN were changed from ?early-onset ulcerative colitis to ulcerative colitis, MONDO:0005101
14 Feb 2024, Gel status: 0
Set publications
Achchuthan Shanmugasundram (Genomics England Curator)Publications for gene: SCGN were set to PMID: 31663849
13 Feb 2024, Gel status: 0
Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes
Hannah Knight (NIHR BioResource - University of Cambridge)gene: SCGN was added gene: SCGN was added to Primary immunodeficiency or monogenic inflammatory bowel disease. Sources: Literature Mode of inheritance for gene: SCGN was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SCGN were set to PMID: 31663849 Phenotypes for gene: SCGN were set to ?early-onset ulcerative colitis Review for gene: SCGN was set to RED