SUGP2

SURP and G-patch domain containing 2, the group of G-patch domain containing

Basic information

Region (hg38): 19:18990888-19034023

Previous symbols: [ "SFRS14" ]

Links

ENSG00000064607 ∙ NCBI:10147 ∙ OMIM:607993 ∙ HGNC:18641 ∙ Uniprot:Q8IX01 ∙ 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 SUGP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUGP2 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						0
missense			53	3		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	3	0

Variants in SUGP2

This is a list of pathogenic ClinVar variants found in the SUGP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18994380-G-A		not specified	Uncertain significance (Nov 22, 2024)
19-18994449-C-T		not specified	Uncertain significance (Jan 29, 2024)
19-18995241-C-T		not specified	Uncertain significance (Mar 21, 2023)
19-18995259-C-T		not specified	Uncertain significance (May 31, 2023)
19-18995273-T-C		not specified	Uncertain significance (Jun 25, 2024)
19-19001632-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-19001633-G-A		not specified	Uncertain significance (Sep 25, 2023)
19-19001659-C-T		not specified	Uncertain significance (Aug 21, 2023)
19-19004263-C-A		not specified	Uncertain significance (Apr 25, 2022)
19-19004321-C-T		not specified	Likely benign (Nov 10, 2023)
19-19004329-C-G		not specified	Uncertain significance (May 06, 2024)
19-19004333-C-T		not specified	Uncertain significance (Nov 18, 2022)
19-19004362-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-19004393-C-T		not specified	Uncertain significance (Dec 27, 2022)
19-19004411-C-T		not specified	Uncertain significance (Jun 21, 2022)
19-19004422-G-A		not specified	Uncertain significance (Jul 14, 2023)
19-19004468-C-T		not specified	Uncertain significance (May 18, 2022)
19-19004524-G-A		not specified	Uncertain significance (Jun 22, 2023)
19-19004528-T-C		not specified	Uncertain significance (Sep 11, 2024)
19-19004536-C-G		not specified	Likely benign (Jun 26, 2024)
19-19008384-C-T		not specified	Uncertain significance (Dec 17, 2023)
19-19008413-A-G		not specified	Uncertain significance (Mar 20, 2023)
19-19008423-T-C		not specified	Uncertain significance (Mar 04, 2024)
19-19009932-G-A		not specified	Uncertain significance (Aug 02, 2021)
19-19009944-C-A		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUGP2	protein_coding	protein_coding	ENST00000601879	9	43136

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000549	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.662	573	619	0.925	0.0000366	7098
Missense in Polyphen		129	188.12	0.68574		2286
Synonymous	-0.480	252	242	1.04	0.0000149	2171
Loss of Function	5.50	3	41.0	0.0732	0.00000240	482

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000663	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in mRNA splicing. {ECO:0000305}.
• Pathway: mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.0986

Intolerance Scores

• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.68

Haploinsufficiency Scores

• pHI: 0.479
• hipred: N
• hipred_score: 0.314
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• 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: Sugp2

Gene ontology

• Biological process: mRNA processing;RNA splicing
• Cellular component: nucleoplasm;nuclear body
• Molecular function: RNA binding