SFMBT2

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

Basic information

Region (hg38): 10:7158623-7411488

Links

ENSG00000198879 ∙ NCBI:57713 ∙ OMIM:615392 ∙ HGNC:20256 ∙ Uniprot:Q5VUG0 ∙ 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 SFMBT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFMBT2 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				1		1
missense			44	3	1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	44	4	1

Variants in SFMBT2

This is a list of pathogenic ClinVar variants found in the SFMBT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-7163805-C-G		not specified	Uncertain significance (May 13, 2024)
10-7163811-C-T		not specified	Uncertain significance (Apr 04, 2024)
10-7163864-T-C		not specified	Uncertain significance (Sep 06, 2022)
10-7171038-C-T		not specified	Uncertain significance (Jun 17, 2022)
10-7171906-C-T		not specified	Uncertain significance (Sep 27, 2022)
10-7171947-G-A		not specified	Uncertain significance (Apr 09, 2024)
10-7171963-C-T		not specified	Likely benign (Nov 10, 2022)
10-7171986-G-A		not specified	Uncertain significance (Feb 21, 2024)
10-7171998-C-A		not specified	Uncertain significance (Jul 27, 2021)
10-7171999-G-A		not specified	Uncertain significance (Jan 16, 2024)
10-7172002-C-T		not specified	Uncertain significance (May 30, 2024)
10-7172038-G-A		not specified	Uncertain significance (Jul 28, 2021)
10-7172067-G-A		not specified	Uncertain significance (Oct 10, 2023)
10-7172097-G-C		not specified	Uncertain significance (Jun 27, 2022)
10-7172098-A-G		not specified	Uncertain significance (Aug 12, 2022)
10-7172500-C-T		not specified	Uncertain significance (Sep 16, 2021)
10-7172521-C-T		not specified	Uncertain significance (Dec 15, 2023)
10-7172544-T-C		not specified	Uncertain significance (Aug 13, 2021)
10-7172548-C-G		not specified	Uncertain significance (Oct 30, 2023)
10-7172548-C-T		not specified	Uncertain significance (Jul 25, 2023)
10-7172563-G-A		not specified	Uncertain significance (Feb 15, 2023)
10-7172565-C-T		not specified	Uncertain significance (Dec 17, 2023)
10-7172581-C-A		not specified	Uncertain significance (Dec 16, 2023)
10-7172602-C-T		not specified	Uncertain significance (Oct 05, 2023)
10-7176049-G-A		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFMBT2	protein_coding	protein_coding	ENST00000361972	20	252865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000610	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	438	520	0.842	0.0000308	5812
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.120
• hipred: Y
• hipred_score: 0.663
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfmbt2

Gene ontology

• Biological process: regulation of transcription, DNA-templated;negative regulation of gene expression;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;aggresome;nuclear speck;intracellular membrane-bounded organelle
• Molecular function: transcription corepressor activity;protein binding;histone binding