ZNF625

zinc finger protein 625, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:12142090-12156734

Links

ENSG00000257591 ∙ NCBI:90589 ∙ ∙ HGNC:30571 ∙ Uniprot:Q96I27 ∙ 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 ZNF625 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF625 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in ZNF625

This is a list of pathogenic ClinVar variants found in the ZNF625 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12145311-C-G		not specified	Uncertain significance (Dec 13, 2022)
19-12145344-G-T		not specified	Uncertain significance (Apr 26, 2023)
19-12145421-T-C		not specified	Uncertain significance (Sep 29, 2023)
19-12145460-C-T		not specified	Uncertain significance (Jan 03, 2022)
19-12145469-G-A		not specified	Uncertain significance (May 09, 2024)
19-12145506-C-T		not specified	Uncertain significance (Feb 27, 2023)
19-12145556-A-G		not specified	Uncertain significance (Apr 25, 2023)
19-12145646-T-C		not specified	Uncertain significance (May 30, 2023)
19-12145859-C-G		not specified	Uncertain significance (Oct 22, 2021)
19-12145974-G-A		not specified	Uncertain significance (Dec 13, 2022)
19-12146099-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-12146123-C-T		not specified	Uncertain significance (Nov 09, 2021)
19-12146186-T-A		not specified	Uncertain significance (May 03, 2023)
19-12147441-C-T		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF625	protein_coding	protein_coding	ENST00000439556	4	16515

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.734	0.255	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	138	193	0.717	0.00000969	2464
Missense in Polyphen		57	80.192	0.71079		1089
Synonymous	-1.53	86	69.8	1.23	0.00000365	657
Loss of Function	1.94	0	4.38	0.00	1.86e-7	56

LoF frequencies by population

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

Intolerance Scores

• loftool: 0.719
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.188
• hipred: N
• hipred_score: 0.218
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0552

Gene Damage Prediction

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

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;protein binding;metal ion binding