SAFB2

scaffold attachment factor B2, the group of RNA binding motif containing

Basic information

Region (hg38): 19:5586998-5624046

Links

ENSG00000130254 ∙ NCBI:9667 ∙ OMIM:608066 ∙ HGNC:21605 ∙ Uniprot:Q14151 ∙ 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 SAFB2 gene.

• Inborn genetic diseases (53 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAFB2 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						0
missense			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	1	0

Variants in SAFB2

This is a list of pathogenic ClinVar variants found in the SAFB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-5587254-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-5587278-G-C		not specified	Uncertain significance (Aug 16, 2021)
19-5587308-C-G		not specified	Uncertain significance (Sep 20, 2023)
19-5587329-C-T		not specified	Uncertain significance (Aug 08, 2023)
19-5587397-C-G		not specified	Uncertain significance (Jun 28, 2022)
19-5587702-C-A		not specified	Uncertain significance (May 10, 2023)
19-5587726-T-C		not specified	Uncertain significance (May 03, 2023)
19-5587741-A-C		not specified	Uncertain significance (Oct 26, 2021)
19-5587928-G-A		not specified	Uncertain significance (Apr 18, 2023)
19-5587948-C-T		not specified	Uncertain significance (Aug 04, 2023)
19-5587966-C-G		not specified	Uncertain significance (May 04, 2022)
19-5587972-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-5590333-C-A		not specified	Uncertain significance (Jul 09, 2021)
19-5590333-C-T		not specified	Uncertain significance (Nov 30, 2022)
19-5590336-C-G		not specified	Uncertain significance (Jan 26, 2023)
19-5590338-C-G		not specified	Uncertain significance (Aug 31, 2022)
19-5590348-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-5590352-G-T		not specified	Uncertain significance (Jan 09, 2024)
19-5590365-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-5590366-G-A		not specified	Uncertain significance (May 11, 2022)
19-5590384-G-C		not specified	Uncertain significance (Mar 29, 2022)
19-5590392-C-T		not specified	Uncertain significance (Mar 11, 2022)
19-5590407-T-A		not specified	Uncertain significance (Mar 11, 2022)
19-5591755-T-A		not specified	Uncertain significance (May 25, 2022)
19-5591786-C-T		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAFB2	protein_coding	protein_coding	ENST00000252542	21	37048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000212	125727	0	11	125738	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.483	515	547	0.942	0.0000385	6174
Missense in Polyphen		87	134.78	0.64548		1344
Synonymous	-0.463	217	209	1.04	0.0000143	1789
Loss of Function	5.62	5	46.2	0.108	0.00000252	586

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000595	0.0000595
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000733	0.0000615
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000338	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to scaffold/matrix attachment region (S/MAR) DNA. Can function as an estrogen receptor corepressor and can also inhibit cell proliferation.

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.352
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.68

Haploinsufficiency Scores

• pHI: 0.178
• hipred: N
• hipred_score: 0.370
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Safb2
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;regulation of mRNA processing;Sertoli cell differentiation;regulation of androgen receptor signaling pathway
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear body;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: RNA binding;protein binding;identical protein binding;sequence-specific DNA binding