SAFB

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

Basic information

Region (hg38): 19:5623034-5668478

Links

ENSG00000160633 ∙ NCBI:6294 ∙ OMIM:602895 ∙ HGNC:10520 ∙ Uniprot:Q15424 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	1	3
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	3	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)
19-5623288-C-G		not specified	Uncertain significance (Aug 17, 2022)
19-5641758-C-G		not specified	Uncertain significance (Dec 16, 2023)
19-5641819-A-G		not specified	Uncertain significance (May 05, 2023)
19-5641851-G-C		not specified	Uncertain significance (Dec 16, 2023)
19-5641912-T-G		not specified	Uncertain significance (Jan 19, 2024)
19-5641923-C-G		not specified	Uncertain significance (Dec 15, 2022)
19-5645366-A-T		not specified	Uncertain significance (Aug 12, 2021)
19-5649932-C-T			Benign (Jul 17, 2018)
19-5651007-G-A		not specified	Uncertain significance (Mar 20, 2023)
19-5653163-T-C		not specified	Uncertain significance (Mar 04, 2024)
19-5654065-A-G		not specified	Likely benign (Nov 13, 2023)
19-5654099-A-C		not specified	Uncertain significance (Oct 05, 2023)
19-5654148-C-A		not specified	Uncertain significance (Feb 28, 2024)
19-5654153-A-G		not specified	Uncertain significance (May 15, 2023)
19-5654392-T-C		not specified	Uncertain significance (Feb 02, 2024)
19-5654435-A-C		not specified	Uncertain significance (Nov 12, 2021)
19-5654437-C-G		not specified	Uncertain significance (Dec 27, 2023)
19-5657292-G-A		not specified	Uncertain significance (May 26, 2023)
19-5657293-T-C		not specified	Uncertain significance (Jan 23, 2024)
19-5657304-A-G		not specified	Uncertain significance (Dec 17, 2023)
19-5661622-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-5661645-A-C		not specified	Uncertain significance (Dec 14, 2023)
19-5661775-G-A		not specified	Uncertain significance (Oct 17, 2023)
19-5661780-G-A		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAFB	protein_coding	protein_coding	ENST00000588852	21	45444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000193	125715	0	1	125716	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	383	521	0.736	0.0000359	6002
Missense in Polyphen		78	137.23	0.5684		1753
Synonymous	-2.11	234	196	1.19	0.0000134	1717
Loss of Function	5.98	2	45.6	0.0439	0.00000254	578

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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