SCAF4

SR-related CTD associated factor 4, the group of RNA binding motif containing

Basic information

Region (hg38): 21:31671000-31732118

Previous symbols: [ "SFRS15" ]

Links

ENSG00000156304 ∙ NCBI:57466 ∙ OMIM:616023 ∙ HGNC:19304 ∙ Uniprot:O95104 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Strong), mode of inheritance: AD
• complex neurodevelopmental disorder (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Fliedner-Zweier syndrome	AD	Cardiovascular	The condition can include cardiovascular as well as other congenital anomalies, and awareness may allow early diagnosis and management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Renal	32730804; 36333968; 37394306

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCAF4 gene.

• Fliedner-Zweier syndrome (3 variants)
• Inborn genetic diseases (3 variants)
• Intellectual disability (2 variants)
• not provided (2 variants)
• Complex neurodevelopmental disorder (1 variants)
• Abnormality of the kidney;Multicystic kidney dysplasia (1 variants)
• SCAF4-associated mental retardation (1 variants)
• Rare syndromic intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAF4 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					1	1
missense			63	15		78
nonsense	3	4	2			9
start loss						0
frameshift	8	4	3	1		16
inframe indel			2	2		4
splice donor/acceptor (+/-2bp)		3	2			5
splice region	1		2	2		5
non coding			1			1
Total	11	11	73	18	1

Variants in SCAF4

This is a list of pathogenic ClinVar variants found in the SCAF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-31671403-C-T		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
21-31671404-G-A		Inborn genetic diseases	Likely benign (Nov 18, 2023)
21-31671407-G-A		Inborn genetic diseases	Uncertain significance (Mar 26, 2024)
21-31671416-CT-C		SCAF4-related disorder	Uncertain significance (Sep 13, 2022)
21-31671445-A-G		Inborn genetic diseases	Likely benign (Oct 01, 2024)
21-31671490-A-G		Inborn genetic diseases	Uncertain significance (Oct 08, 2024)
21-31671496-G-A		Inborn genetic diseases	Uncertain significance (Oct 24, 2023)
21-31671585-CCTGT-C		Neurodevelopmental disorder	Likely benign (Jun 15, 2023)
21-31671619-G-T			Uncertain significance (Jan 16, 2024)
21-31671627-CTTCT-C		See cases	Uncertain significance (Jan 27, 2021)
21-31671643-T-A			Uncertain significance (Jul 23, 2023)
21-31671657-A-C		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
21-31671665-C-G		Inborn genetic diseases	Uncertain significance (Apr 20, 2023)
21-31671667-C-G			Uncertain significance (Feb 10, 2021)
21-31671676-T-C		Inborn genetic diseases	Uncertain significance (Aug 20, 2024)
21-31671686-A-G			Uncertain significance (Jan 03, 2023)
21-31671700-T-A			Uncertain significance (May 30, 2024)
21-31671714-G-C		Inborn genetic diseases	Uncertain significance (Apr 05, 2023)
21-31671716-G-A			Uncertain significance (Apr 08, 2022)
21-31671718-C-A			Uncertain significance (Dec 23, 2023)
21-31671724-C-T		Inborn genetic diseases	Uncertain significance (Dec 10, 2024)
21-31671738-C-G		Inborn genetic diseases	Uncertain significance (Nov 11, 2024)
21-31671743-C-T		SCAF4-related disorder	Uncertain significance (Sep 16, 2024)
21-31671758-C-T		SCAF4-related disorder	Likely benign (Jul 10, 2024)
21-31671760-C-T		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAF4	protein_coding	protein_coding	ENST00000286835	20	61043

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.00e-8	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	518	658	0.787	0.0000363	7413
Missense in Polyphen		47	112.87	0.41641		1494
Synonymous	-0.890	245	228	1.07	0.0000130	2372
Loss of Function	6.92	2	59.6	0.0335	0.00000356	614

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000184
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.0000551	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act to physically and functionally link transcription and pre-mRNA processing. {ECO:0000250}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: -1.21
• rvis_percentile_EVS: 5.68

Haploinsufficiency Scores

• pHI: 0.764
• hipred: Y
• hipred_score: 0.662
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• 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: Scaf4

Gene ontology

• Cellular component: nucleoplasm
• Molecular function: RNA binding