SCAPER

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

Basic information

Region (hg38): 15:76347904-76905444

Previous symbols: [ "ZNF291" ]

Links

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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 51.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_020843.4	NP_065894.2	31	yes	-
ENST00000563290.6	ENSP00000454973.1	31	yes	-
NM_001145923.2	NP_001139395.1	25	-	-
NM_001353009.2	NP_001339938.1	31	-	-

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder and retinitis pigmentosa; IDDRP (Moderate), mode of inheritance: AR
• intellectual developmental disorder and retinitis pigmentosa; IDDRP (Strong), mode of inheritance: AR
• retinitis pigmentosa (Supportive), mode of inheritance: AD
• Bardet-Biedl syndrome (Supportive), mode of inheritance: AR
• neurodevelopmental disorder (Strong), 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 (161 variants)
• SCAPER-related_disorder (89 variants)
• not_provided (55 variants)
• Intellectual_developmental_disorder_and_retinitis_pigmentosa%3B_IDDRP (35 variants)
• Retinal_dystrophy (13 variants)
• Optic_atrophy (5 variants)
• Moderate_intellectual_disability (3 variants)
• Rod-cone_dystrophy (3 variants)
• Obesity (1 variants)
• Syndromic_retinitis_pigmentosa (1 variants)
• Schizophrenia (1 variants)
• Attention_deficit_hyperactivity_disorder (1 variants)
• Abnormal_speech_pattern (1 variants)
• Intellectual_disability (1 variants)
• Retinitis_pigmentosa (1 variants)
• Short_stature (1 variants)
• Bardet-Biedl_syndrome_1 (1 variants)
• Pigmentary_retinopathy (1 variants)
• Brachydactyly (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. These statistics are base on transcript: NM_020843.4. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	37	7	46
missense		1	190	16	4	211
nonsense	2	6	2			10
start loss						0
frameshift	5	7	2			14
splice donor/acceptor (+/-2bp)	1	3	10			14
Total	8	17	206	53	11

Highest pathogenic variant AF is 0.000035961282

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
		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

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

Gene ontology

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