ZNF354A

zinc finger protein 354A, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 5:178711512-178730659

Previous symbols: [ "TCF17" ]

Links

ENSG00000169131 ∙ NCBI:6940 ∙ OMIM:602444 ∙ HGNC:11628 ∙ Uniprot:O60765 ∙ 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 ZNF354A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF354A 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				3		3
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	4	0

Variants in ZNF354A

This is a list of pathogenic ClinVar variants found in the ZNF354A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-178712112-T-A		not specified	Uncertain significance (Jun 12, 2023)
5-178712134-T-C		not specified	Uncertain significance (Feb 08, 2023)
5-178712148-G-A		not specified	Uncertain significance (Jul 19, 2023)
5-178712233-G-A		not specified	Uncertain significance (Jul 06, 2021)
5-178712378-C-G			Likely benign (Nov 01, 2022)
5-178712441-T-G			Likely benign (Sep 17, 2017)
5-178712446-T-G		not specified	Uncertain significance (May 26, 2024)
5-178712592-C-T		not specified	Uncertain significance (Dec 21, 2022)
5-178712631-C-T		not specified	Uncertain significance (Feb 28, 2024)
5-178712808-T-C		not specified	Uncertain significance (Feb 27, 2023)
5-178712835-T-A		not specified	Uncertain significance (Oct 26, 2021)
5-178712895-T-C		not specified	Uncertain significance (Nov 15, 2021)
5-178712945-T-G			Likely benign (Mar 01, 2022)
5-178713123-C-T		not specified	Likely benign (Oct 22, 2021)
5-178713154-A-G		not specified	Uncertain significance (Jan 05, 2022)
5-178713190-G-A		not specified	Uncertain significance (Oct 12, 2021)
5-178713241-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-178713318-G-A		not specified	Uncertain significance (Sep 28, 2022)
5-178713345-T-C		not specified	Uncertain significance (Jul 22, 2022)
5-178713358-G-A		not specified	Uncertain significance (Oct 14, 2023)
5-178713376-A-G		not specified	Uncertain significance (Sep 16, 2021)
5-178713445-C-G		not specified	Uncertain significance (Oct 13, 2023)
5-178713541-T-A		not specified	Uncertain significance (Feb 05, 2024)
5-178713562-C-T		not specified	Uncertain significance (Nov 28, 2023)
5-178713573-G-A		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF354A	protein_coding	protein_coding	ENST00000335815	4	19111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000564	0.994	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.995	265	315	0.842	0.0000161	3975
Missense in Polyphen		59	112.14	0.52613		1418
Synonymous	0.446	105	111	0.946	0.00000556	1099
Loss of Function	2.44	13	26.6	0.489	0.00000171	340

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.705
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.154
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.803

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp354a

Gene ontology

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