SFMBT2

protein-coding

Scm like with four mbt domains 2, the group of MBT domain containing|Sterile alpha motif domain containing

Gene summary

Enables histone binding activity. Involved in negative regulation of gene expression. Located in nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001387889.1

Inheritance

—

ClinVar variants

U:124B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr10:7,158,624-7,411,488

External References & Databases

Ensembl (ENSG00000198879)

Transcript & Mutation Effects

hg38 • Region Span ~252.9 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 SFMBT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 130

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001387889.1. 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		2
missense			123 clinvar	7 clinvar		130
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	124	9	0	133

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001387889.1	RefSeq	NP_001374818.1	20	MANE Select
ENST00000397167.6	Ensembl	ENSP00000380353.1	20	MANE Select
NM_001018039.1	RefSeq	NP_001018049.1	20	Standard
NM_001029880.3	RefSeq	NP_001025051.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
negative regulation of gene expression
negative regulation of nucleic acid-templated transcription

Molecular Function

transcription corepressor activity
protein binding
histone binding

Cellular Component

nucleus
aggresome
nuclear speck
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361972
Coding exons: 20
Length: 252865
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.28	438	520	0.842	0.0000308	5812
Missense (PolyPhen)		164	229.29	0.71527		2533
Synonymous	-0.506	225	216	1.04	0.0000152	1721
Loss of Function	5.80	7	52.2	0.134	0.00000296	589

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional repressor of HOXB13 gene. {ECO:0000269|PubMed:23385818}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.386
RVIS EVS: -0.62
RVIS percentile EVS: 17.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.266

Gene Damage Prediction

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