ZNF648

zinc finger protein 648, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:182054570-182061712

Links

ENSG00000179930 ∙ NCBI:127665 ∙ ∙ HGNC:18190 ∙ Uniprot:Q5T619 ∙ 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 ZNF648 gene.

• not_specified (86 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF648 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001009992.1. 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						0
missense			85	1		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	85	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF648	protein_coding	protein_coding	ENST00000339948	1	7143

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-12	0.0128	125638	1	109	125748	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.240	363	376	0.965	0.0000244	3683
Missense in Polyphen		99	108.71	0.91069		1112
Synonymous	0.970	156	172	0.906	0.0000125	1157
Loss of Function	-0.541	17	14.8	1.15	6.34e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000420
Ashkenazi Jewish	0.00188	0.00189
East Asian	0.000945	0.000870
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000437	0.000396
Middle Eastern	0.000945	0.000870
South Asian	0.000496	0.000457
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• loftool: 0.647
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.55

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.285

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp648

Gene ontology

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