SCAPER

S-phase cyclin A associated protein in the ER, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 15:76347903-76905444

Previous symbols: [ "ZNF291" ]

Links

ENSG00000140386 ∙ NCBI:49855 ∙ OMIM:611611 ∙ HGNC:13081 ∙ Uniprot:Q9BY12 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Supportive), mode of inheritance: AD
• Bardet-Biedl syndrome (Supportive), mode of inheritance: AR
• intellectual developmental disorder and retinitis pigmentosa; IDDRP (Moderate), mode of inheritance: AR
• intellectual developmental disorder and retinitis pigmentosa; IDDRP (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder and retinitis pigmentosa	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	Neurologic; Ophthalmologic	28794130

ClinVar

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

• Inborn genetic diseases (51 variants)
• not provided (43 variants)
• Intellectual developmental disorder and retinitis pigmentosa; IDDRP (22 variants)
• SCAPER-related condition (2 variants)
• 6 conditions (1 variants)
• Attention deficit hyperactivity disorder;Intellectual disability, moderate;Rod-cone dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAPER 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				11	8	19
missense			49	5	5	59
nonsense	1					1
start loss					1	1
frameshift	4	3				7
inframe indel						0
splice donor/acceptor (+/-2bp)		2	1			3
splice region				6	4	10
non coding		1	4	1	6	12
Total	5	6	54	17	20

Highest pathogenic variant AF is 0.0000197

Variants in SCAPER

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

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

Position	Type	Phenotype	Significance	ClinVar
15-76348636-T-G		Inborn genetic diseases	Uncertain significance (Jul 28, 2022)
15-76348652-A-G		Inborn genetic diseases	Uncertain significance (Jul 12, 2023)
15-76348662-G-T		Inborn genetic diseases	Uncertain significance (Jan 30, 2024)
15-76351235-A-G		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
15-76351252-G-C		Inborn genetic diseases	Uncertain significance (Aug 15, 2023)
15-76351277-C-G		Inborn genetic diseases	Uncertain significance (Jun 17, 2022)
15-76353977-C-G		Inborn genetic diseases	Uncertain significance (Aug 21, 2023)
15-76354014-T-G		Inborn genetic diseases	Uncertain significance (Nov 17, 2023)
15-76354026-CA-C		Intellectual developmental disorder and retinitis pigmentosa; IDDRP	Uncertain significance (Apr 04, 2024)
15-76354030-G-A			Likely benign (Dec 31, 2019)
15-76354038-A-G		Inborn genetic diseases	Uncertain significance (Mar 12, 2024)
15-76354114-G-C		SCAPER-related disorder	Benign (Dec 31, 2019)
15-76354135-G-A			Likely benign (Aug 01, 2023)
15-76376178-T-C		Inborn genetic diseases	Uncertain significance (Aug 02, 2022)
15-76376193-C-G		Inborn genetic diseases	Uncertain significance (Apr 18, 2023)
15-76376199-C-T		Inborn genetic diseases	Uncertain significance (Dec 21, 2021)
15-76376206-T-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 24, 2023)
15-76376237-T-C		SCAPER-related disorder	Benign/Likely benign (Sep 01, 2022)
15-76376308-TAG-T		Intellectual developmental disorder and retinitis pigmentosa; IDDRP	Likely pathogenic (Apr 30, 2019)
15-76381375-T-C		Intellectual developmental disorder and retinitis pigmentosa; IDDRP • SCAPER-related disorder	Benign (Nov 07, 2021)
15-76381427-C-T		Intellectual disability, moderate;Rod-cone dystrophy • Intellectual developmental disorder and retinitis pigmentosa; IDDRP	Pathogenic/Likely pathogenic (Nov 20, 2018)
15-76381433-A-G		Inborn genetic diseases	Uncertain significance (Apr 13, 2022)
15-76381444-G-T		SCAPER-related disorder	Benign (Dec 31, 2019)
15-76381446-T-C		Inborn genetic diseases	Likely benign (Feb 07, 2023)
15-76381451-T-C		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAPER	protein_coding	protein_coding	ENST00000563290	31	557260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00880	0.991	124598	0	43	124641	0.000173

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.72	522	729	0.716	0.0000391	9188
Missense in Polyphen		160	299.43	0.53435		3822
Synonymous	-0.558	257	246	1.05	0.0000123	2585
Loss of Function	6.03	20	77.1	0.259	0.00000428	933

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000341	0.000339
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.000168	0.000167
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000221	0.000204
Middle Eastern	0.000168	0.000167
South Asian	0.000241	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: CCNA2/CDK2 regulatory protein that transiently maintains CCNA2 in the cytoplasm. {ECO:0000269|PubMed:17698606}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.984
• rvis_EVS: 0.65
• rvis_percentile_EVS: 84.18

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.527
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.195

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scaper

Gene ontology

• Cellular component: nucleus;endoplasmic reticulum;cytosol
• Molecular function: nucleic acid binding;zinc ion binding