SF3A2 (splicing factor 3a subunit 2) - Rat Genome Database

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Gene: SF3A2 (splicing factor 3a subunit 2) Homo sapiens
Analyze
Symbol: SF3A2
Name: splicing factor 3a subunit 2
RGD ID: 1318510
HGNC Page HGNC:10766
Description: Enables RNA binding activity. Involved in U2-type prespliceosome assembly. Located in nucleus. Part of U2 snRNP; U2-type precatalytic spliceosome; and catalytic step 2 spliceosome.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: pre-mRNA splicing factor SF3A, subunit 2; PRP11; PRPF11; SAP 62; SAP62; SF3a66; spliceosome associated protein 62; spliceosome-associated protein 62; splicing factor 3a, subunit 2, 66kD; splicing factor 3a, subunit 2, 66kDa
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: SF3A2P1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38192,236,824 - 2,248,655 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl192,236,824 - 2,248,655 (+)EnsemblGRCh38hg38GRCh38
GRCh37192,236,823 - 2,248,654 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36192,187,816 - 2,199,678 (+)NCBINCBI36Build 36hg18NCBI36
Build 34192,187,815 - 2,199,677NCBI
Celera192,170,993 - 2,182,854 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef192,007,853 - 2,019,794 (+)NCBIHuRef
CHM1_1192,236,320 - 2,248,181 (+)NCBICHM1_1
T2T-CHM13v2.0192,210,388 - 2,222,298 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
2. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8211113   PMID:8541848   PMID:8718683   PMID:9016565   PMID:9576861   PMID:9710584   PMID:9731529   PMID:10385517   PMID:10882114   PMID:11500380   PMID:11533230   PMID:11602354  
PMID:11991638   PMID:12226669   PMID:12234937   PMID:12477932   PMID:15057824   PMID:15142036   PMID:15231748   PMID:15316075   PMID:15489334   PMID:15647371   PMID:16009940   PMID:16055720  
PMID:17332742   PMID:19615732   PMID:20360068   PMID:20379614   PMID:20467437   PMID:21145461   PMID:21349847   PMID:21873635   PMID:22174317   PMID:22365833   PMID:22658674   PMID:22681889  
PMID:22939629   PMID:23398456   PMID:24104479   PMID:24163370   PMID:24304693   PMID:24550385   PMID:24711643   PMID:24916648   PMID:24981860   PMID:25798074   PMID:26186194   PMID:26344197  
PMID:26420826   PMID:26472337   PMID:26496610   PMID:26527279   PMID:26725010   PMID:27684187   PMID:27976729   PMID:28077445   PMID:28302793   PMID:28514442   PMID:28973437   PMID:29180619  
PMID:29298432   PMID:29360106   PMID:29509190   PMID:29777862   PMID:29844126   PMID:30021884   PMID:30110629   PMID:30404004   PMID:30463901   PMID:30475206   PMID:30804502   PMID:30890647  
PMID:31059266   PMID:31478661   PMID:31527615   PMID:31553912   PMID:31586073   PMID:31744343   PMID:31751430   PMID:31980649   PMID:32129710   PMID:32203420   PMID:32296183   PMID:32416067  
PMID:32494006   PMID:32513696   PMID:32687490   PMID:32707033   PMID:32807901   PMID:32994395   PMID:33545068   PMID:33742100   PMID:33863777   PMID:33961781   PMID:34373451   PMID:34822310  
PMID:35013218   PMID:35256949   PMID:35271311   PMID:35439318   PMID:35509820   PMID:35530310   PMID:35545034   PMID:35652658   PMID:35776542   PMID:35831314   PMID:35850772   PMID:35914814  
PMID:35944360   PMID:35987950   PMID:36215168   PMID:36424410   PMID:36526897   PMID:36574265   PMID:36629882   PMID:36732831   PMID:36797247   PMID:37827155   PMID:38113892  


Genomics

Comparative Map Data
SF3A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38192,236,824 - 2,248,655 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl192,236,824 - 2,248,655 (+)EnsemblGRCh38hg38GRCh38
GRCh37192,236,823 - 2,248,654 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36192,187,816 - 2,199,678 (+)NCBINCBI36Build 36hg18NCBI36
Build 34192,187,815 - 2,199,677NCBI
Celera192,170,993 - 2,182,854 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef192,007,853 - 2,019,794 (+)NCBIHuRef
CHM1_1192,236,320 - 2,248,181 (+)NCBICHM1_1
T2T-CHM13v2.0192,210,388 - 2,222,298 (+)NCBIT2T-CHM13v2.0
Sf3a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,634,569 - 80,640,756 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1080,634,032 - 80,640,758 (+)EnsemblGRCm39 Ensembl
GRCm381080,798,735 - 80,804,922 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,798,198 - 80,804,924 (+)EnsemblGRCm38mm10GRCm38
MGSCv371080,261,480 - 80,267,667 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361080,201,713 - 80,207,943 (+)NCBIMGSCv36mm8
Celera1081,817,105 - 81,823,292 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Sf3a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,560,182 - 9,566,205 (-)NCBIGRCr8
mRatBN7.278,909,507 - 8,916,104 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,909,507 - 8,915,530 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,788,187 - 11,794,212 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,663,692 - 13,669,717 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,530,215 - 11,536,177 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,777,826 - 11,784,373 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,777,826 - 11,783,849 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0711,945,541 - 11,952,001 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,419,996 - 10,426,019 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1710,419,995 - 10,426,019 (-)NCBI
Celera77,092,245 - 7,098,268 (-)NCBICelera
Cytogenetic Map7q11NCBI
Sf3a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554955,896,648 - 5,904,056 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554955,896,648 - 5,904,287 (-)NCBIChiLan1.0ChiLan1.0
SF3A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2206,621,344 - 6,633,517 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1195,850,687 - 5,862,859 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0191,247,812 - 1,259,984 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1192,219,326 - 2,231,343 (+)NCBIpanpan1.1PanPan1.1panPan2
SF3A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12056,789,450 - 56,796,004 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2056,788,577 - 56,795,262 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2056,584,524 - 56,595,530 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02057,522,321 - 57,533,330 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2057,522,324 - 57,532,588 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12056,574,342 - 56,585,347 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02057,059,470 - 57,070,468 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02057,259,967 - 57,270,974 (-)NCBIUU_Cfam_GSD_1.0
Sf3a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118216,492,208 - 216,499,676 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365881,335,166 - 1,342,575 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365881,335,143 - 1,342,573 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SF3A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,410,602 - 76,415,776 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1276,404,882 - 76,414,901 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2277,041,418 - 77,049,953 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SF3A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.162,034,892 - 2,047,653 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl62,041,384 - 2,047,542 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660816,673,327 - 6,689,638 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sf3a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248286,638,660 - 6,644,788 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248286,638,546 - 6,646,529 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SF3A2
20 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19p13.3(chr19:259395-2555149)x3 copy number gain See cases [RCV000051044] Chr19:259395..2555149 [GRCh38]
Chr19:259395..2555147 [GRCh37]
Chr19:210395..2506147 [NCBI36]
Chr19:19p13.3		 pathogenic
GRCh38/hg38 19p13.3(chr19:1565575-4108128)x3 copy number gain See cases [RCV000052878] Chr19:1565575..4108128 [GRCh38]
Chr19:1565574..4108126 [GRCh37]
Chr19:1516574..4059126 [NCBI36]
Chr19:19p13.3		 pathogenic
GRCh38/hg38 19p13.3-13.2(chr19:1972245-9648879)x3 copy number gain See cases [RCV000052879] Chr19:1972245..9648879 [GRCh38]
Chr19:1972244..9759555 [GRCh37]
Chr19:1923244..9620555 [NCBI36]
Chr19:19p13.3-13.2		 pathogenic
GRCh38/hg38 19p13.3-13.2(chr19:265917-8564134)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052876]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052876]|See cases [RCV000052876] Chr19:265917..8564134 [GRCh38]
Chr19:265917..8629018 [GRCh37]
Chr19:216917..8535018 [NCBI36]
Chr19:19p13.3-13.2		 pathogenic
GRCh38/hg38 19p13.3(chr19:233565-4699472)x3 copy number gain See cases [RCV000052575] Chr19:233565..4699472 [GRCh38]
Chr19:233565..4699484 [GRCh37]
Chr19:184565..4650484 [NCBI36]
Chr19:19p13.3		 pathogenic
GRCh38/hg38 19p13.3(chr19:1727562-2306496)x1 copy number loss See cases [RCV000053941] Chr19:1727562..2306496 [GRCh38]
Chr19:1727561..2306495 [GRCh37]
Chr19:1678561..2257495 [NCBI36]
Chr19:19p13.3		 pathogenic
GRCh38/hg38 19p13.3(chr19:1549144-4288720)x1 copy number loss See cases [RCV000134795] Chr19:1549144..4288720 [GRCh38]
Chr19:1549143..4288717 [GRCh37]
Chr19:1500143..4239717 [NCBI36]
Chr19:19p13.3		 pathogenic
GRCh38/hg38 19p13.3(chr19:421537-2897921)x3 copy number gain See cases [RCV000134894] Chr19:421537..2897921 [GRCh38]
Chr19:421537..2897919 [GRCh37]
Chr19:372537..2848919 [NCBI36]
Chr19:19p13.3		 likely pathogenic
GRCh38/hg38 19p13.3(chr19:1351163-2555149)x3 copy number gain See cases [RCV000136880] Chr19:1351163..2555149 [GRCh38]
Chr19:1351162..2555147 [GRCh37]
Chr19:1302162..2506147 [NCBI36]
Chr19:19p13.3		 uncertain significance
GRCh38/hg38 19p13.3(chr19:259395-6795611)x3 copy number gain See cases [RCV000142627] Chr19:259395..6795611 [GRCh38]
Chr19:259395..6795622 [GRCh37]
Chr19:210395..6746622 [NCBI36]
Chr19:19p13.3		 pathogenic
GRCh37/hg19 19p13.3(chr19:1952590-2698712)x3 copy number gain See cases [RCV000239912] Chr19:1952590..2698712 [GRCh37]
Chr19:19p13.3		 uncertain significance
GRCh37/hg19 19p13.3(chr19:277373-2555164)x3 copy number gain See cases [RCV000240507] Chr19:277373..2555164 [GRCh37]
Chr19:19p13.3		 pathogenic
GRCh37/hg19 19p13.3(chr19:260911-2256387)x3 copy number gain See cases [RCV002285065] Chr19:260911..2256387 [GRCh37]
Chr19:19p13.3		 pathogenic
GRCh37/hg19 19p13.3(chr19:259395-3152419) copy number gain Global developmental delay [RCV000626520] Chr19:259395..3152419 [GRCh37]
Chr19:19p13.3		 likely pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888) copy number gain See cases [RCV000512296] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43		 pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888)x3 copy number gain See cases [RCV000511289] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43		 pathogenic|uncertain significance
GRCh37/hg19 19p13.3(chr19:260911-3200875)x3 copy number gain not provided [RCV000684094] Chr19:260911..3200875 [GRCh37]
Chr19:19p13.3		 pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-59097160)x3 copy number gain not provided [RCV000752444] Chr19:260912..59097160 [GRCh37]
Chr19:19p13.3-q13.43		 pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:68029-59110290)x3 copy number gain not provided [RCV000752439] Chr19:68029..59110290 [GRCh37]
Chr19:19p13.3-q13.43		 pathogenic
GRCh37/hg19 19p13.3(chr19:2245444-2250236)x1 copy number loss not provided [RCV000739982] Chr19:2245444..2250236 [GRCh37]
Chr19:19p13.3		 benign
GRCh37/hg19 19p13.3(chr19:2245444-2251817)x1 copy number loss not provided [RCV000739983] Chr19:2245444..2251817 [GRCh37]
Chr19:19p13.3		 benign
NM_007165.5(SF3A2):c.1148C>A (p.Ala383Asp) single nucleotide variant Inborn genetic diseases [RCV003268942] Chr19:2248299 [GRCh38]
Chr19:2248298 [GRCh37]
Chr19:19p13.3		 uncertain significance
NC_000019.9:g.1406030_3597207dup duplication Neurodevelopmental disorder [RCV000787423] Chr19:1406030..3597207 [GRCh37]
Chr19:19p13.3		 uncertain significance
Single allele deletion Internal malformations [RCV000787421] Chr19:2229488..4004142 [GRCh37]
Chr19:19p13.3		 uncertain significance
GRCh37/hg19 19p13.3(chr19:260911-4788357)x3 copy number gain not provided [RCV000846988] Chr19:260911..4788357 [GRCh37]
Chr19:19p13.3		 pathogenic
GRCh37/hg19 19p13.3(chr19:260911-3501271)x3 copy number gain not provided [RCV001007025] Chr19:260911..3501271 [GRCh37]
Chr19:19p13.3		 pathogenic
GRCh37/hg19 19p13.3(chr19:260912-4384674)x3 copy number gain See cases [RCV001007443] Chr19:260912..4384674 [GRCh37]
Chr19:19p13.3		 pathogenic
GRCh37/hg19 19p13.3(chr19:1075192-2256387)x3 copy number gain not provided [RCV001007026] Chr19:1075192..2256387 [GRCh37]
Chr19:19p13.3		 likely pathogenic
NM_007165.5(SF3A2):c.1250C>T (p.Ser417Leu) single nucleotide variant Inborn genetic diseases [RCV003197820] Chr19:2248401 [GRCh38]
Chr19:2248400 [GRCh37]
Chr19:19p13.3		 uncertain significance
GRCh37/hg19 19p13.3(chr19:1973753-2380699)x3 copy number gain not provided [RCV001834492] Chr19:1973753..2380699 [GRCh37]
Chr19:19p13.3		 uncertain significance
NC_000019.9:g.(?_589946)_(5696788_?)dup duplication not provided [RCV003113597] Chr19:589946..5696788 [GRCh37]
Chr19:19p13.3		 uncertain significance
NC_000019.9:g.(?_1456055)_(2456931_?)dup duplication Progressive myoclonic epilepsy type 9 [RCV003122897] Chr19:1456055..2456931 [GRCh37]
Chr19:19p13.3		 uncertain significance
NC_000019.9:g.(?_589946)_(4818389_?)dup duplication not provided [RCV003105391] Chr19:589946..4818389 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.665G>C (p.Ser222Thr) single nucleotide variant Inborn genetic diseases [RCV003257615] Chr19:2247816 [GRCh38]
Chr19:2247815 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.737C>T (p.Pro246Leu) single nucleotide variant Inborn genetic diseases [RCV002901392] Chr19:2247888 [GRCh38]
Chr19:2247887 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.576G>T (p.Glu192Asp) single nucleotide variant Inborn genetic diseases [RCV002997737] Chr19:2247623 [GRCh38]
Chr19:2247622 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.1298C>G (p.Pro433Arg) single nucleotide variant Inborn genetic diseases [RCV002905115] Chr19:2248449 [GRCh38]
Chr19:2248448 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.824C>T (p.Pro275Leu) single nucleotide variant Inborn genetic diseases [RCV002823286] Chr19:2247975 [GRCh38]
Chr19:2247974 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.653C>T (p.Pro218Leu) single nucleotide variant Inborn genetic diseases [RCV002951391] Chr19:2247804 [GRCh38]
Chr19:2247803 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.1163C>T (p.Pro388Leu) single nucleotide variant Inborn genetic diseases [RCV002940311] Chr19:2248314 [GRCh38]
Chr19:2248313 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.1234C>A (p.Pro412Thr) single nucleotide variant Inborn genetic diseases [RCV002809493] Chr19:2248385 [GRCh38]
Chr19:2248384 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.374C>T (p.Ser125Leu) single nucleotide variant Inborn genetic diseases [RCV002988967] Chr19:2246771 [GRCh38]
Chr19:2246770 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.797C>T (p.Pro266Leu) single nucleotide variant Inborn genetic diseases [RCV002652834] Chr19:2247948 [GRCh38]
Chr19:2247947 [GRCh37]
Chr19:19p13.3		 uncertain significance
NC_000019.9:g.(?_1206913)_(3771740_?)dup duplication not provided [RCV003154903] Chr19:1206913..3771740 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.1247C>T (p.Pro416Leu) single nucleotide variant Inborn genetic diseases [RCV003197647] Chr19:2248398 [GRCh38]
Chr19:2248397 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.707C>G (p.Pro236Arg) single nucleotide variant Inborn genetic diseases [RCV003205829] Chr19:2247858 [GRCh38]
Chr19:2247857 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.949C>A (p.Pro317Thr) single nucleotide variant Inborn genetic diseases [RCV003344724] Chr19:2248100 [GRCh38]
Chr19:2248099 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.61G>A (p.Glu21Lys) single nucleotide variant Inborn genetic diseases [RCV003376322] Chr19:2243479 [GRCh38]
Chr19:2243478 [GRCh37]
Chr19:19p13.3		 uncertain significance
NM_007165.5(SF3A2):c.1161C>A (p.His387Gln) single nucleotide variant Inborn genetic diseases [RCV003362244] Chr19:2248312 [GRCh38]
Chr19:2248311 [GRCh37]
Chr19:19p13.3		 uncertain significance
GRCh37/hg19 19p13.3-13.2(chr19:260912-7246777)x3 copy number gain not provided [RCV003485190] Chr19:260912..7246777 [GRCh37]
Chr19:19p13.3-13.2		 pathogenic
GRCh37/hg19 19p13.3(chr19:2123255-2258285)x3 copy number gain not specified [RCV003986119] Chr19:2123255..2258285 [GRCh37]
Chr19:19p13.3		 uncertain significance
GRCh37/hg19 19p13.3(chr19:1648089-2302433)x3 copy number gain not specified [RCV003986124] Chr19:1648089..2302433 [GRCh37]
Chr19:19p13.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2546
Count of miRNA genes:903
Interacting mature miRNAs:1107
Transcripts:ENST00000221494, ENST00000586396, ENST00000587637, ENST00000589118, ENST00000590034, ENST00000591121, ENST00000592314, ENST00000592839
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
GDB:182516  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3p21.1UniSTS
Cytogenetic Map19p13.3UniSTS
Cytogenetic Map4q21.21UniSTS
Cytogenetic Map19p13.1UniSTS
Cytogenetic Map10q23.33UniSTS
Cytogenetic Map2q37.3UniSTS
Cytogenetic Map11q13.1UniSTS
Cytogenetic Map17q25.1UniSTS
Cytogenetic Map21q22.3UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2429 2948 1681 583 1921 425 4353 2167 3636 383 1446 1607 171 1204 2787 3
Low 3 36 42 40 26 39 2 26 73 35 3 1 1 1 1
Below cutoff 2 3 2 1 9 1 2 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000221494   ⟹   ENSP00000221494
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl192,236,824 - 2,248,655 (+)Ensembl
RefSeq Acc Id: ENST00000586396   ⟹   ENSP00000466634
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl192,237,794 - 2,246,802 (+)Ensembl
RefSeq Acc Id: ENST00000587637
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl192,245,509 - 2,247,206 (+)Ensembl
RefSeq Acc Id: ENST00000589118
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl192,236,832 - 2,245,186 (+)Ensembl
RefSeq Acc Id: ENST00000590034
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl192,243,382 - 2,244,953 (+)Ensembl
RefSeq Acc Id: ENST00000592314
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl192,236,860 - 2,247,878 (+)Ensembl
RefSeq Acc Id: ENST00000592839
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl192,236,853 - 2,245,838 (+)Ensembl
RefSeq Acc Id: NM_007165   ⟹   NP_009096
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38192,236,824 - 2,248,655 (+)NCBI
GRCh37192,236,816 - 2,248,678 (+)ENTREZGENE
Build 36192,187,816 - 2,199,678 (+)NCBI Archive
HuRef192,007,853 - 2,019,794 (+)ENTREZGENE
CHM1_1192,236,320 - 2,248,181 (+)NCBI
T2T-CHM13v2.0192,210,388 - 2,222,298 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_009096   ⟸   NM_007165
- UniProtKB: D6W605 (UniProtKB/Swiss-Prot),   B2RBU1 (UniProtKB/Swiss-Prot),   O75245 (UniProtKB/Swiss-Prot),   Q15428 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000466634   ⟸   ENST00000586396
RefSeq Acc Id: ENSP00000221494   ⟸   ENST00000221494
Protein Domains
Matrin-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q15428-F1-model_v2 AlphaFold Q15428 1-464 view protein structure

Promoters
RGD ID:6796031
Promoter ID:HG_KWN:28453
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   Lymphoblastoid
Transcripts:NM_007165
Position:
Human AssemblyChrPosition (strand)Source
Build 36192,187,591 - 2,188,091 (+)MPROMDB
RGD ID:6852260
Promoter ID:EP73936
Type:initiation region
Name:HS_SF3A2
Description:Splicing factor 3a, subunit 2, 66kDa.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Mammalian gene collection (MGC) full-length cDNA cloning
Position:
Human AssemblyChrPosition (strand)Source
Build 36192,187,863 - 2,187,923EPD
RGD ID:7237913
Promoter ID:EPDNEW_H24702
Type:initiation region
Name:SF3A2_3
Description:splicing factor 3a subunit 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H24704  EPDNEW_H24703  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38192,236,390 - 2,236,450EPDNEW
RGD ID:7237917
Promoter ID:EPDNEW_H24703
Type:initiation region
Name:SF3A2_2
Description:splicing factor 3a subunit 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H24702  EPDNEW_H24704  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38192,236,538 - 2,236,598EPDNEW
RGD ID:7237915
Promoter ID:EPDNEW_H24704
Type:initiation region
Name:SF3A2_1
Description:splicing factor 3a subunit 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H24702  EPDNEW_H24703  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38192,236,846 - 2,236,906EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10766 AgrOrtholog
COSMIC SF3A2 COSMIC
Ensembl Genes ENSG00000104897 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000221494 ENTREZGENE
  ENST00000221494.10 UniProtKB/Swiss-Prot
  ENST00000586396.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.2690 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
GTEx ENSG00000104897 GTEx
HGNC ID HGNC:10766 ENTREZGENE
Human Proteome Map SF3A2 Human Proteome Map
InterPro Matrin/U1-C_Znf_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Matrin/U1-like-C_Znf_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SF3A2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:8175 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 8175 ENTREZGENE
OMIM 600796 OMIM
PANTHER SPLICING FACTOR 3A SUBUNIT 2 UniProtKB/Swiss-Prot
  SPLICING FACTOR 3A SUBUNIT 2 UniProtKB/Swiss-Prot
  SPLICING FACTOR 3A SUBUNIT 2 UniProtKB/TrEMBL
  SPLICING FACTOR 3A SUBUNIT 2 UniProtKB/TrEMBL
Pfam SF3A2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-met UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA35684 PharmGKB
PROSITE ZF_MATRIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CactinC_cactus UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_U1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B2RBU1 ENTREZGENE
  D6W605 ENTREZGENE
  K7EMT0_HUMAN UniProtKB/TrEMBL
  O75245 ENTREZGENE
  Q05DF2_HUMAN UniProtKB/TrEMBL
  Q15428 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B2RBU1 UniProtKB/Swiss-Prot
  D6W605 UniProtKB/Swiss-Prot
  O75245 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-17 SF3A2  splicing factor 3a subunit 2  SF3A2  splicing factor 3a, subunit 2, 66kDa  Symbol and/or name change 5135510 APPROVED