SNAPC4

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

Basic information

Region (hg38): 9:136375566-136400176

Links

ENSG00000165684 ∙ NCBI:6621 ∙ OMIM:602777 ∙ HGNC:11137 ∙ Uniprot:Q5SXM2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic; Ophthalmologic	36965478

ClinVar

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

• Inborn genetic diseases (106 variants)
• not provided (6 variants)
• not specified (2 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.

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				3	2	5
missense			96	12		108
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	96	15	2

Variants in SNAPC4

This is a list of pathogenic ClinVar variants found in the SNAPC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136376372-C-T		Inborn genetic diseases	Uncertain significance (Feb 10, 2023)
9-136376450-G-A		Inborn genetic diseases	Uncertain significance (May 26, 2023)
9-136376477-G-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
9-136377574-G-A		Inborn genetic diseases	Uncertain significance (Aug 17, 2022)
9-136377596-G-A		Inborn genetic diseases	Uncertain significance (Mar 22, 2023)
9-136377606-A-G		not specified	Benign (Mar 29, 2016)
9-136377614-G-A		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
9-136377646-G-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2021)
9-136377647-A-T		Inborn genetic diseases	Likely benign (Jul 14, 2021)
9-136377653-C-T		Inborn genetic diseases	Uncertain significance (May 09, 2023)
9-136377676-T-C		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
9-136377715-G-A		Inborn genetic diseases	Uncertain significance (Dec 19, 2023)
9-136377728-G-A		Inborn genetic diseases	Uncertain significance (Jan 18, 2023)
9-136377751-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
9-136377764-G-A		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
9-136377790-G-A		Inborn genetic diseases	Uncertain significance (Sep 17, 2021)
9-136377799-G-A		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
9-136377811-C-T		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
9-136377827-C-G		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
9-136377829-A-C		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
9-136377887-G-A			Likely benign (Feb 01, 2023)
9-136377892-C-T		Long QT syndrome	Likely benign (-)
9-136377941-G-A		Inborn genetic diseases	Uncertain significance (Nov 27, 2023)
9-136377990-C-G		Inborn genetic diseases	Uncertain significance (Feb 17, 2022)
9-136377997-T-C		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNAPC4	protein_coding	protein_coding	ENST00000298532	22	23221

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.65e-29	0.0349	125536	0	211	125747	0.000839

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.08	957	868	1.10	0.0000553	9282
Missense in Polyphen		215	234.03	0.9187		2746
Synonymous	-4.51	496	384	1.29	0.0000257	3158
Loss of Function	1.71	53	68.3	0.776	0.00000383	706

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00225	0.00224
Ashkenazi Jewish	0.000314	0.000298
East Asian	0.00156	0.00152
Finnish	0.000143	0.0000924
European (Non-Finnish)	0.000757	0.000721
Middle Eastern	0.00156	0.00152
South Asian	0.00121	0.00118
Other	0.000717	0.000652

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

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

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