SUB1

SUB1 regulator of transcription

Basic information

Region (hg38): 5:32531632-32604079

Links

ENSG00000113387 ∙ NCBI:10923 ∙ OMIM:600503 ∙ HGNC:19985 ∙ Uniprot:P53999 ∙ 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 SUB1 gene.

• not provided (2 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUB1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	1	1	1

Variants in SUB1

This is a list of pathogenic ClinVar variants found in the SUB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-32591634-C-T			Likely benign (Jul 26, 2018)
5-32591651-A-G		not specified	Uncertain significance (Dec 14, 2023)
5-32591670-T-A		not specified	Uncertain significance (Sep 16, 2021)
5-32598951-T-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUB1	protein_coding	protein_coding	ENST00000265073	4	72447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.892	0.107	124336	0	2	124338	0.00000804

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	33	64.6	0.511	0.00000311	846
Missense in Polyphen		6	14.878	0.40327		217
Synonymous	0.510	19	22.0	0.862	0.00000120	217
Loss of Function	2.49	0	7.23	0.00	3.06e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA). {ECO:0000269|PubMed:16605275, ECO:0000269|PubMed:16689930, ECO:0000269|PubMed:7628453, ECO:0000269|PubMed:8062391, ECO:0000269|PubMed:8062392, ECO:0000269|PubMed:9360603, ECO:0000269|PubMed:9482861}.

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.314
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.730
• hipred: Y
• hipred_score: 0.752
• ghis: 0.709

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sub1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of transcription initiation from RNA polymerase II promoter;SMAD protein signal transduction
• Cellular component: nucleus;transcription factor complex;nucleolus;extracellular exosome
• Molecular function: DNA-binding transcription activator activity, RNA polymerase II-specific;single-stranded DNA binding;transcription coactivator activity;RNA binding;protein binding;identical protein binding;sequence-specific double-stranded DNA binding