SAFB2

protein-coding

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

Gene summary

The protein encoded by this gene, along with its paralog (scaffold attachment factor B1), is a repressor of estrogen receptor alpha. The encoded protein binds scaffold/matrix attachment region (S/MAR) DNA and is involved in cell cycle regulation, apoptosis, differentiation, the stress response, and regulation of immune genes. [provided by RefSeq, May 2016]

MANE transcript

NM_014649.3

Inheritance

—

ClinVar variants

U:161B:5

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr19:5,586,981-5,624,046

External References & Databases

Ensembl (ENSG00000130254)

Transcript & Mutation Effects

hg38 • Region Span ~37.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SAFB2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 145

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014649.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			148 clinvar	4 clinvar		152
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	161	5	0	166

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014649.3	RefSeq	NP_055464.1	21	MANE Select
ENST00000252542.9	Ensembl	ENSP00000252542.3	21	MANE Select
ENST00000590262.1	Ensembl	ENSP00000468454.1	4	Standard
ENST00000591120.1	Ensembl	ENSP00000468505.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
regulation of mRNA processing
Sertoli cell differentiation
regulation of androgen receptor signaling pathway

Molecular Function

RNA binding
protein binding
identical protein binding
sequence-specific DNA binding

Cellular Component

nucleus
nucleoplasm
cytoplasm
nuclear body
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252542
Coding exons: 21
Length: 37048
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125738
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.483	515	547	0.942	0.0000385	6174
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000073	0.000062	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.992

Gene Damage Prediction

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