ZNF250

zinc finger protein 250, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 8:144876497-144902168

Previous symbols: [ "ZNF647" ]

Links

ENSG00000196150 ∙ NCBI:58500 ∙ ∙ HGNC:13044 ∙ Uniprot:P15622 ∙ 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 ZNF250 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF250 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			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in ZNF250

This is a list of pathogenic ClinVar variants found in the ZNF250 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144881586-C-T		not specified	Uncertain significance (Apr 23, 2024)
8-144881712-C-T		not specified	Uncertain significance (Jul 14, 2021)
8-144881754-T-C		not specified	Likely benign (Oct 26, 2021)
8-144881919-C-T		not specified	Uncertain significance (Jan 03, 2024)
8-144881943-C-T		not specified	Uncertain significance (Sep 27, 2021)
8-144882067-G-C		not specified	Uncertain significance (Aug 08, 2023)
8-144882076-C-G		not specified	Uncertain significance (Apr 17, 2024)
8-144882087-C-T		not specified	Uncertain significance (Dec 04, 2023)
8-144882159-T-C		not specified	Likely benign (Apr 07, 2023)
8-144882327-C-T		not specified	Uncertain significance (Oct 05, 2023)
8-144882348-C-T		not specified	Uncertain significance (Jun 11, 2021)
8-144882398-C-A		not specified	Uncertain significance (Jan 10, 2023)
8-144882618-T-A		not specified	Uncertain significance (May 27, 2022)
8-144882638-G-A		not specified	Uncertain significance (May 13, 2024)
8-144882674-C-T		not specified	Uncertain significance (Dec 15, 2022)
8-144882675-G-C		not specified	Uncertain significance (Jan 05, 2022)
8-144882724-A-T		not specified	Uncertain significance (Aug 15, 2023)
8-144882779-G-A		not specified	Uncertain significance (Mar 01, 2023)
8-144882794-G-A		not specified	Likely benign (Jan 04, 2024)
8-144886879-T-C		not specified	Uncertain significance (Sep 17, 2021)
8-144889586-T-C		not specified	Uncertain significance (Jan 26, 2022)
8-144889602-C-T		not specified	Uncertain significance (Jun 22, 2023)
8-144890065-A-C		not specified	Uncertain significance (Sep 14, 2022)
8-144890339-G-C		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF250	protein_coding	protein_coding	ENST00000292579	5	50922

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.278	0.722	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	206	325	0.635	0.0000183	3713
Missense in Polyphen		66	148.13	0.44556		1691
Synonymous	0.217	126	129	0.976	0.00000764	1046
Loss of Function	3.24	5	21.1	0.238	9.72e-7	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0942

Intolerance Scores

• loftool: 0.522
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.347
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.900

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp647

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding