SNAPC4

small nuclear RNA activating complex polypeptide 4, the group of Myb/SANT domain containing|SNAP complex

Basic information

Region (hg38): 9:136375567-136400176

Links

ENSG00000165684NCBI:6621OMIM:602777HGNC:11137Uniprot:Q5SXM2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction (Moderate), mode of inheritance: AR
  • neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunctionARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingMusculoskeletal; Neurologic; Ophthalmologic36965478

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNAPC4 gene.

  • Inborn_genetic_diseases (287 variants)
  • not_provided (24 variants)
  • Neurodevelopmental_disorder_with_motor_regression,_progressive_spastic_paraplegia,_and_oromotor_dysfunction (8 variants)
  • SNAPC4_related_condition (2 variants)
  • Long_QT_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNAPC4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003086.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
10
missense
4
clinvar
264
clinvar
32
clinvar
1
clinvar
301
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
2
clinvar
4
Total 7 2 264 42 1

Highest pathogenic variant AF is 0.0000855184

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SNAPC4protein_codingprotein_codingENST00000298532 2223221
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.65e-290.034912553602111257470.000839
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.089578681.100.00005539282
Missense in Polyphen215234.030.91872746
Synonymous-4.514963841.290.00002573158
Loss of Function1.715368.30.7760.00000383706

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002250.00224
Ashkenazi Jewish0.0003140.000298
East Asian0.001560.00152
Finnish0.0001430.0000924
European (Non-Finnish)0.0007570.000721
Middle Eastern0.001560.00152
South Asian0.001210.00118
Other0.0007170.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box. {ECO:0000269|PubMed:12621023, ECO:0000269|PubMed:9418884}.;
Pathway
Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

pRec
0.0850

Intolerance Scores

loftool
0.896
rvis_EVS
0.32
rvis_percentile_EVS
72.76

Haploinsufficiency Scores

pHI
0.0854
hipred
N
hipred_score
0.314
ghis
0.509

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
H
gene_indispensability_pred
E
gene_indispensability_score
0.853

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Snapc4
Phenotype
limbs/digits/tail phenotype; skeleton phenotype;

Zebrafish Information Network

Gene name
snapc4
Affected structure
intrahepatic bile duct
Phenotype tag
abnormal
Phenotype quality
hypoplastic

Gene ontology

Biological process
regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription by RNA polymerase III;snRNA transcription;snRNA transcription by RNA polymerase II;snRNA transcription by RNA polymerase III
Cellular component
nucleus;nucleoplasm;snRNA-activating protein complex
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity