SNRPG

protein-coding

small nuclear ribonucleoprotein polypeptide G, the group of Sm spliceosomal proteins

Gene summary

The protein encoded by this gene is a component of the U1, U2, U4, and U5 small nuclear ribonucleoprotein complexes, precursors of the spliceosome. The encoded protein may also be a part of the U7 small nuclear ribonucleoprotein complex, which participates in the processing of the 3' end of histone transcripts. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

MANE transcript

NM_003096.4

Inheritance

—

ClinVar variants

U:7B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr2:70,281,362-70,293,740

External References & Databases

Ensembl (ENSG00000143977)

Transcript & Mutation Effects

hg38 • Region Span ~12.4 kb

Loading mutation effect viewer...

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 SNRPG variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003096.4. 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				1 clinvar		1
missense			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	7	1	0	8

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003096.4	RefSeq	NP_003087.1	4	MANE Select
ENST00000272348.7	Ensembl	ENSP00000272348.2	4	MANE Select
NM_001317165.2	RefSeq	NP_001304094.1	5	Standard
NM_001317166.2	RefSeq	NP_001304095.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
mRNA Processing
Gene expression (Transcription)
snRNP Assembly
RNA Polymerase II Transcription

Biological Process

spliceosomal complex assembly
spliceosomal snRNP assembly
mRNA splicing, via spliceosome
termination of RNA polymerase II transcription
histone mRNA metabolic process

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
spliceosomal complex
U5 snRNP
U7 snRNP

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272348
Coding exons: 4
Length: 12410
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.54	14	42.1	0.333	0.00000211	501
Missense (PolyPhen)		0	4.2991	0		63
Synonymous	-1.12	18	12.9	1.40	6.25e-7	122
Loss of Function	2.15	0	5.40	0.00	3.23e-7	64

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. {ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:23333303}.;

Recessive Scores

pRec: 0.123

Intolerance Scores

RVIS EVS: 0.12
RVIS percentile EVS: 62.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.902

Gene Damage Prediction

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