SCAF8

SR-related CTD associated factor 8, the group of RNA binding motif containing

Basic information

Region (hg38): 6:154733377-154834244

Previous symbols: [ "RBM16" ]

Links

ENSG00000213079 ∙ NCBI:22828 ∙ OMIM:616024 ∙ HGNC:20959 ∙ Uniprot:Q9UPN6 ∙ 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 SCAF8 gene.

• Inborn genetic diseases (27 variants)
• Autism spectrum disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAF8 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			26	1		27
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in SCAF8

This is a list of pathogenic ClinVar variants found in the SCAF8 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-154792863-A-G		not specified	Uncertain significance (Sep 16, 2021)
6-154792965-G-A		not specified	Uncertain significance (May 31, 2023)
6-154795017-G-A		not specified	Uncertain significance (Aug 02, 2023)
6-154795039-A-G		not specified	Uncertain significance (Aug 17, 2021)
6-154805444-A-T		not specified	Uncertain significance (Oct 20, 2023)
6-154808170-A-G		not specified	Uncertain significance (Aug 16, 2022)
6-154808185-T-C		not specified	Uncertain significance (Oct 02, 2023)
6-154808786-G-A		not specified	Uncertain significance (Dec 13, 2023)
6-154808792-G-A		not specified	Uncertain significance (Aug 02, 2021)
6-154810029-G-A		not specified	Uncertain significance (May 31, 2023)
6-154810101-G-A		not specified	Uncertain significance (Jun 22, 2023)
6-154810184-C-T		not specified	Uncertain significance (Oct 05, 2023)
6-154818585-T-C		not specified	Uncertain significance (Dec 22, 2023)
6-154824252-G-A		not specified	Uncertain significance (Feb 27, 2023)
6-154827217-C-A		not specified	Uncertain significance (Dec 03, 2021)
6-154830982-G-A		not specified	Uncertain significance (Nov 20, 2023)
6-154831027-C-A		not specified	Uncertain significance (Dec 19, 2023)
6-154831029-G-A		not specified	Likely benign (Jul 14, 2021)
6-154832041-C-T		not specified	Uncertain significance (Jan 18, 2023)
6-154832100-A-G		not specified	Uncertain significance (Sep 16, 2021)
6-154832280-C-G		not specified	Uncertain significance (Jun 24, 2022)
6-154832311-T-C		not specified	Uncertain significance (Dec 13, 2023)
6-154832359-G-A		not specified	Uncertain significance (Jul 20, 2022)
6-154832385-G-A		not specified	Uncertain significance (Jun 29, 2023)
6-154832427-C-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAF8	protein_coding	protein_coding	ENST00000367178	20	100734

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.10e-9	125556	0	3	125559	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	560	702	0.798	0.0000369	8245
Missense in Polyphen		164	219.65	0.74663		2540
Synonymous	-2.62	293	241	1.21	0.0000127	2570
Loss of Function	7.27	2	65.5	0.0305	0.00000383	709

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000892	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in mRNA processing. {ECO:0000269|PubMed:11101529}.

Intolerance Scores

• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.34

Haploinsufficiency Scores

• pHI: 0.198
• hipred: Y
• hipred_score: 0.591
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• 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: Scaf8

Gene ontology

• Biological process: termination of RNA polymerase II transcription;mRNA polyadenylation;RNA splicing
• Cellular component: nucleoplasm;spliceosomal complex;cytoplasm;nuclear matrix
• Molecular function: RNA polymerase II complex binding;mRNA binding;protein binding;RNA polymerase core enzyme binding