ZNF513

zinc finger protein 513, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 2:27377234-27380790

Links

ENSG00000163795 ∙ NCBI:130557 ∙ OMIM:613598 ∙ HGNC:26498 ∙ Uniprot:Q8N8E2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis pigmentosa 58 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 58	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	Ophthalmologic	20797688; 20227676

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF513 gene.

• not provided (317 variants)
• Retinitis pigmentosa (49 variants)
• Inborn genetic diseases (28 variants)
• Retinitis Pigmentosa, Dominant (22 variants)
• Retinitis pigmentosa 58 (4 variants)
• ZNF513-related condition (3 variants)
• not specified (2 variants)
• Retinal dystrophy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF513 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			4	84	2	90
missense			181	3		184
nonsense			1			1
start loss			1			1
frameshift		1	4			5
inframe indel			4	1		5
splice donor/acceptor (+/-2bp)						0
splice region			3	4		7
non coding			25	27		52
Total	0	1	220	115	2

Variants in ZNF513

This is a list of pathogenic ClinVar variants found in the ZNF513 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27377269-ATAAGT-A		Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)
2-27377291-A-T		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-27377320-C-T		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-27377328-C-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-27377371-C-T		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-27377372-G-A		Retinitis Pigmentosa, Dominant • Retinitis pigmentosa	Benign/Likely benign (Jan 13, 2018)
2-27377381-C-T		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-27377411-T-C		Retinitis Pigmentosa, Dominant • Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-27377416-C-T		Retinitis Pigmentosa, Dominant • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-27377485-G-A		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-27377491-G-A		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-27377516-G-A		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
2-27377530-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
2-27377546-C-A			Uncertain significance (Oct 06, 2023)
2-27377554-G-C			Uncertain significance (Jun 13, 2022)
2-27377555-T-C			Uncertain significance (Jan 21, 2022)
2-27377567-G-A			Uncertain significance (Nov 12, 2022)
2-27377570-C-T		Retinitis pigmentosa	Uncertain significance (Jul 07, 2023)
2-27377571-G-A			Uncertain significance (Jul 22, 2023)
2-27377577-C-T			Uncertain significance (Nov 06, 2022)
2-27377579-G-A			Uncertain significance (Nov 12, 2022)
2-27377591-G-A			Uncertain significance (Feb 03, 2022)
2-27377593-T-C		Retinal dystrophy	Conflicting classifications of pathogenicity (Oct 01, 2023)
2-27377594-G-A			Uncertain significance (Dec 31, 2019)
2-27377594-G-T			Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF513	protein_coding	protein_coding	ENST00000323703	4	3560

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.816	0.184	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.530	313	341	0.919	0.0000228	3470
Missense in Polyphen		49	41.479	1.1813		377
Synonymous	-2.33	172	137	1.25	0.00000815	1174
Loss of Function	3.37	3	18.8	0.160	0.00000116	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000807	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator that plays a role in retinal development and maintenance. {ECO:0000269|PubMed:20797688}.

Intolerance Scores

• loftool: 0.204
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.53

Haploinsufficiency Scores

• pHI: 0.505
• hipred: Y
• hipred_score: 0.531
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp513

Zebrafish Information Network

• Gene name: znf513a
• Affected structure: retinal rod cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;visual perception;regulation of gene expression;response to stimulus;retina development in camera-type eye
• Cellular component: nucleus;histone methyltransferase complex
• Molecular function: RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;transcription regulatory region DNA binding;metal ion binding