ZNF410

zinc finger protein 410, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 14:73886616-73932521

Links

ENSG00000119725 ∙ NCBI:57862 ∙ OMIM:619427 ∙ HGNC:20144 ∙ Uniprot:Q86VK4 ∙ 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 ZNF410 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF410 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				1		1
missense			21			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	21	1	0

Variants in ZNF410

This is a list of pathogenic ClinVar variants found in the ZNF410 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-73893840-A-C		not specified	Uncertain significance (Mar 31, 2023)
14-73893845-C-T		not specified	Uncertain significance (Aug 02, 2023)
14-73893890-C-G		not specified	Uncertain significance (Jun 10, 2024)
14-73893903-C-T		not specified	Uncertain significance (Feb 23, 2023)
14-73896328-A-G		not specified	Uncertain significance (Nov 09, 2022)
14-73896381-C-T		not specified	Uncertain significance (Jul 06, 2021)
14-73896388-A-G		not specified	Uncertain significance (Aug 02, 2021)
14-73896439-C-T		not specified	Uncertain significance (Oct 05, 2023)
14-73896468-A-G		not specified	Uncertain significance (Feb 02, 2022)
14-73898116-C-G		not specified	Uncertain significance (Sep 27, 2022)
14-73898223-C-T		not specified	Uncertain significance (Apr 26, 2023)
14-73903972-A-C		not specified	Uncertain significance (Aug 10, 2023)
14-73904006-T-C		not specified	Likely benign (Jan 16, 2024)
14-73904010-C-T		not specified	Uncertain significance (Mar 23, 2023)
14-73904011-C-T		not specified	Uncertain significance (Apr 07, 2023)
14-73904047-T-C		not specified	Uncertain significance (Nov 13, 2023)
14-73904930-G-A		not specified	Uncertain significance (Jun 18, 2024)
14-73904932-A-T		not specified	Uncertain significance (Nov 10, 2022)
14-73909418-G-T		not specified	Uncertain significance (May 28, 2023)
14-73921092-G-T		not specified	Uncertain significance (Jan 03, 2024)
14-73922107-G-A		not specified	Uncertain significance (Apr 25, 2022)
14-73923419-G-A		not specified	Uncertain significance (Dec 03, 2021)
14-73923419-G-T		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF410	protein_coding	protein_coding	ENST00000442160	12	45895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.353	0.647	125730	0	14	125744	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	164	274	0.598	0.0000141	3353
Missense in Polyphen		57	99.87	0.57074		1189
Synonymous	0.299	97	101	0.962	0.00000495	1016
Loss of Function	3.68	6	26.4	0.227	0.00000127	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000308	0.000308
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that activates transcription of matrix-remodeling genes such as MMP1 during fibroblast senescence. {ECO:0000269|PubMed:12370286}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.638
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.699
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.841

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp410

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