SUGP1

SURP and G-patch domain containing 1, the group of G-patch domain containing|Spliceosomal A complex

Basic information

Region (hg38): 19:19276018-19320509

Previous symbols: [ "SF4" ]

Links

ENSG00000105705 ∙ NCBI:57794 ∙ OMIM:607992 ∙ HGNC:18643 ∙ Uniprot:Q8IWZ8 ∙ 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 SUGP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUGP1 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				2	1	3
missense			46	2		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	4	1

Variants in SUGP1

This is a list of pathogenic ClinVar variants found in the SUGP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19276667-G-C		not specified	Uncertain significance (May 15, 2023)
19-19276967-G-A		not specified	Uncertain significance (Dec 09, 2023)
19-19277021-A-C		not specified	Uncertain significance (Nov 23, 2022)
19-19277040-A-C		not specified	Uncertain significance (Jan 03, 2024)
19-19277848-T-C		not specified	Uncertain significance (Jan 24, 2023)
19-19278700-T-C		not specified	Uncertain significance (Dec 17, 2023)
19-19279317-G-T		not specified	Uncertain significance (Mar 24, 2023)
19-19279326-C-A		not specified	Uncertain significance (Dec 15, 2022)
19-19279371-A-G		not specified	Uncertain significance (Aug 02, 2022)
19-19279376-G-A			Benign (Jan 02, 2019)
19-19280253-G-C		not specified	Uncertain significance (Dec 27, 2023)
19-19280253-G-T			Uncertain significance (Jan 19, 2017)
19-19297001-A-G		not specified	Uncertain significance (Apr 18, 2023)
19-19297024-T-C		not specified	Uncertain significance (May 14, 2024)
19-19297043-G-C		not specified	Uncertain significance (Nov 21, 2022)
19-19297055-T-C		not specified	Uncertain significance (Dec 22, 2023)
19-19297106-C-T		not specified	Likely benign (May 21, 2024)
19-19297124-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-19297150-G-C		not specified	Uncertain significance (Oct 04, 2022)
19-19297151-G-A		not specified	Uncertain significance (Apr 06, 2024)
19-19297169-C-A		not specified	Uncertain significance (Jul 31, 2023)
19-19297217-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-19297226-G-A		not specified	Uncertain significance (Feb 13, 2024)
19-19297235-C-G		not specified	Uncertain significance (Dec 19, 2022)
19-19297258-C-A		not specified	Uncertain significance (Apr 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUGP1	protein_coding	protein_coding	ENST00000247001	14	44827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00432	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	332	400	0.830	0.0000245	4239
Missense in Polyphen		93	132.3	0.70297		1426
Synonymous	0.329	156	161	0.967	0.0000110	1211
Loss of Function	4.74	4	33.7	0.119	0.00000162	397

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000320	0.000277
European (Non-Finnish)	0.0000108	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in pre-mRNA splicing.
• Pathway: mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• rvis_EVS: -1.02
• rvis_percentile_EVS: 8

Haploinsufficiency Scores

• pHI: 0.120
• hipred: Y
• hipred_score: 0.775
• ghis: 0.608

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sugp1

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: nucleoplasm;spliceosomal complex
• Molecular function: RNA binding;protein binding