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GeneBe

SAFB

scaffold attachment factor B, the group of RNA binding motif containing

Basic information

Region (hg38): 19:5623034-5668478

Links

ENSG00000160633NCBI:6294OMIM:602895HGNC:10520Uniprot:Q15424AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAFB gene.

  • Inborn genetic diseases (14 variants)
  • not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAFB 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
2
clinvar
1
clinvar
3
missense
15
clinvar
15
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 15 2 1

Variants in SAFB

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

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

Position Type Phenotype Significance ClinVar
19-5623216-C-T not specified Uncertain significance (Dec 22, 2023)3157493
19-5623288-C-G not specified Uncertain significance (Aug 17, 2022)2307689
19-5641758-C-G not specified Uncertain significance (Dec 16, 2023)3157513
19-5641819-A-G not specified Uncertain significance (May 05, 2023)2544618
19-5641851-G-C not specified Uncertain significance (Dec 16, 2023)3157514
19-5641912-T-G not specified Uncertain significance (Jan 19, 2024)3157515
19-5641923-C-G not specified Uncertain significance (Dec 15, 2022)2335463
19-5645366-A-T not specified Uncertain significance (Aug 12, 2021)2347596
19-5649932-C-T Benign (Jul 17, 2018)735932
19-5651007-G-A not specified Uncertain significance (Mar 20, 2023)2527093
19-5653163-T-C not specified Uncertain significance (Mar 04, 2024)3157494
19-5654065-A-G not specified Likely benign (Nov 13, 2023)3157495
19-5654099-A-C not specified Uncertain significance (Oct 05, 2023)3157496
19-5654148-C-A not specified Uncertain significance (Feb 28, 2024)3157497
19-5654153-A-G not specified Uncertain significance (May 15, 2023)2546320
19-5654392-T-C not specified Uncertain significance (Feb 02, 2024)3157498
19-5654435-A-C not specified Uncertain significance (Nov 12, 2021)2261138
19-5654437-C-G not specified Uncertain significance (Dec 27, 2023)3157499
19-5657292-G-A not specified Uncertain significance (May 26, 2023)2567911
19-5657293-T-C not specified Uncertain significance (Jan 23, 2024)3157500
19-5657304-A-G not specified Uncertain significance (Dec 17, 2023)3157501
19-5661622-G-A not specified Uncertain significance (Dec 08, 2023)3157502
19-5661645-A-C not specified Uncertain significance (Dec 14, 2023)3157503
19-5661775-G-A not specified Uncertain significance (Oct 17, 2023)3157504
19-5661780-G-A not specified Uncertain significance (Feb 28, 2024)3157505

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAFBprotein_codingprotein_codingENST00000588852 2145444
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00000193125715011257160.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.143835210.7360.00003596002
Missense in Polyphen78137.230.56841753
Synonymous-2.112341961.190.00001341717
Loss of Function5.98245.60.04390.00000254578

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008790.00000879
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds to scaffold/matrix attachment region (S/MAR) DNA and forms a molecular assembly point to allow the formation of a 'transcriptosomal' complex (consisting of SR proteins and RNA polymerase II) coupling transcription and RNA processing (By similarity). Can function as an estrogen receptor corepressor and can also bind to the HSP27 promoter and decrease its transcription. When associated with RBMX, binds to and stimulates transcription from the SREBF1 promoter (By similarity). Can inhibit cell proliferation. {ECO:0000250}.;
Pathway
Structural Pathway of Interleukin 1 (IL-1);Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

pRec
0.157

Intolerance Scores

loftool
0.0204
rvis_EVS
-1.62
rvis_percentile_EVS
2.93

Haploinsufficiency Scores

pHI
0.207
hipred
Y
hipred_score
0.743
ghis
0.665

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
H
gene_indispensability_pred
E
gene_indispensability_score
0.920

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Safb
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; skeleton phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
chromatin organization;regulation of transcription by RNA polymerase II;intracellular estrogen receptor signaling pathway;regulation of growth;hormone metabolic process;positive regulation of transcription by RNA polymerase II;regulation of mRNA processing
Cellular component
nucleus;nucleoplasm
Molecular function
RNA polymerase II proximal promoter sequence-specific DNA binding;chromatin binding;double-stranded DNA binding;RNA binding;protein binding;sequence-specific DNA binding