SUGP2

protein-coding

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

Gene summary

This gene encodes a member of the arginine/serine-rich family of splicing factors. The encoded protein functions in mRNA processing. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]

Previous symbols:

SFRS14

MANE transcript

NM_001017392.5

Inheritance

—

ClinVar variants

U:158B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr19:18,990,888-19,034,023

External References & Databases

Ensembl (ENSG00000064607)

Transcript & Mutation Effects

hg38 • Region Span ~43.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SUGP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 155

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001017392.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			152 clinvar	7 clinvar		159
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	158	7	0	165

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 85 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001017392.5	RefSeq	NP_001017392.2	9	MANE Select
ENST00000452918.7	Ensembl	ENSP00000389380.1	9	MANE Select
NM_001321697.2	RefSeq	NP_001308626.1	9	Standard
NM_001321698.1	RefSeq	NP_001308627.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mRNA Processing

Biological Process

mRNA processing
RNA splicing

Molecular Function

RNA binding

Cellular Component

nucleoplasm
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000601879
Coding exons: 9
Length: 43136
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.662	573	619	0.925	0.0000366	7098
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in mRNA splicing. {ECO:0000305}.;

Recessive Scores

pRec: 0.0986

Intolerance Scores

RVIS EVS: 0.39
RVIS percentile EVS: 75.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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