SFMBT1

Scm like with four mbt domains 1, the group of MBT domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 3:52903572-53046750

Links

ENSG00000163935 ∙ NCBI:51460 ∙ OMIM:607319 ∙ HGNC:20255 ∙ Uniprot:Q9UHJ3 ∙ 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 SFMBT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFMBT1 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	3	4
missense					2	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	5

Variants in SFMBT1

This is a list of pathogenic ClinVar variants found in the SFMBT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52916190-G-A			Likely benign (Aug 01, 2023)
3-52920549-G-A			Benign (Aug 02, 2017)
3-52928240-G-A			Benign (Jun 05, 2018)
3-52928298-C-A			Benign (Apr 24, 2018)
3-52930407-A-G			Benign (Aug 02, 2017)
3-52932300-A-G			Benign (Aug 02, 2017)
3-52999277-CTACGTGAAGGAGGCCAAGCACAGCCGTGGACACCGGCCTGAAGGCTGGGAAAGGAGCCGACGCCCCACCTCCTCTGACCAGGCCTGCGGGGAGGAGCCACCCACGCGCCACAGCAAGTCCTGGACCTGGCCCTGCATTCCAGGGTGGGGCAGGGAGGCTGGATTCTGAGAGAGCTGCTTCCGGATTGCGTTGGGGTAGTCAAGGAGCTCGGGACATCGCAGGGGAGGCAAAAAGCCTTGGCCAGTGCTCTTTTGGTGTATCCCTTCAGCTTCCAGAGGGGAAGCCACACCCTGATGCTATGTTCAAACGCTCCAGAAGACAGGAGTTCGTGTCCTTGCCCCTAACCACTGCTGTGGATGTCACTGGCCAAAGGTCATGAGGGGAGTGGGCCACATGAGTGGCCACTTGCCATGACTCCCTGAGCAGGGTGAGCCCCCACTCATCCTGTGCCATGTTATGTTTCCACCCAAGCAGCAGGGTAGGAGGCACAATGAGTGCCCATTCCTCTCCCTGATGGGCCCCCCAAGCTCTACAGACCAAGCAAGGAGACCCCATGACCCATGGCATGAAATCATCTTGAAGTTTTTGCTTTTTTTTTGGAGACAGAGTATCGCTCTGTCGCCCAGGCTGGAATGCAGTGGCACAATCTCGGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCATGAGTAGTTGGGACTACAGGCATGTGCCACCACATCAGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTGTTAGCCAGGATGGTCTTGATTTCCTGACCTCGTGATCCGCCCACCCCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCCAGCCTACTCTTACATTTTTTTAGGTTTTTATTTACTCACTGCTTTAAGCATACACGACACTTCGGTTTTATTCCTCCCTTTGTAATGTTTTTTCTCTTAAGCCACTTTTTTTTTTTTTTGCAATGCCTTCCTCTTTGAAAGCATTAAAAAAACAGTATTTTGTTTATGTTTCAACAACAACAAAGAGGACTTAATGTCTGGCACACTAAAATATTTACCAATAAAACAAACTGATATTTGGAATTTTTTTAAGTTTTAAAAGTGTGGTCACTGTATTGTGATCACACAATTACATTAGGAAAATGTCTTATTCTTAGAGATGTACATTAAAGTATTAAGAGTACTGAGTTATAATGTCTGCAATAGAGCCTCAAATGTTTCACAGGGGACTATATAAATACATATATATGCCTATATATACATATATTACATATATACACATATATAAAAGACAAAGAGAGAAAGCAAACAGTGATTCTAGGTGAAAGACAAAGTGAGAACTCAGCAAAAACGTAAATTAGTACAGGTTTGTTGGAAAGCAATGTGATGACATCTCAAAATTGGAAGAAATTTACAAAAACTAAAACATGCCTAATGCATGTCCTTTGACCCAACACCCCTTCTAGGAATTTATCTTTAAAAAACTCACACAAGACCACAAAGCAAGAAAGGGTATTAATTACAAAAATTTTTTAATGGTTTAATACTCAAATATCTACCAATAGGTGGTTAGGTAAATAAGTTATTGCAAATGCTTAAAATGAAAAAAAATATATGAAAAGAAGAAAGGGGTGTGGGTACAGATGAAACCGCATTGGCTGTGAGTTTATTACAGAAGCAATCTTTGAATAATGGATATTTGGATGTTCA-C		Normal pregnancy • Preeclampsia • Large for gestational age	not provided (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFMBT1	protein_coding	protein_coding	ENST00000394752	20	143179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.936	0.0641	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	357	484	0.738	0.0000259	5684
Missense in Polyphen		87	153.22	0.56779		1932
Synonymous	1.00	156	173	0.903	0.00000925	1634
Loss of Function	5.25	9	48.4	0.186	0.00000232	589

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000803	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone-binding protein, which is part of various corepressor complexes. Mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. Plays a role during myogenesis: required for the maintenance of undifferentiated states of myogenic progenitor cells via interaction with MYOD1. Interaction with MYOD1 leads to the recruitment of associated corepressors and silencing of MYOD1 target genes. Part of the SLC complex in germ cells, where it may play a role during spermatogenesis. {ECO:0000269|PubMed:17599839, ECO:0000269|PubMed:23349461, ECO:0000269|PubMed:23592795}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.324
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.63

Haploinsufficiency Scores

• pHI: 0.804
• hipred: Y
• hipred_score: 0.619
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfmbt1

Gene ontology

• Biological process: chromatin organization;spermatogenesis;cell differentiation;negative regulation of transcription, DNA-templated;negative regulation of muscle organ development
• Cellular component: nucleus;nucleoplasm
• Molecular function: transcription corepressor activity;protein binding;histone binding