ZFAND3

zinc finger AN1-type containing 3, the group of Zinc fingers AN1-type

Basic information

Region (hg38): 6:37819726-38154624

Previous symbols: [ "TEX27" ]

Links

ENSG00000156639 ∙ NCBI:60685 ∙ OMIM:607455 ∙ HGNC:18019 ∙ Uniprot:Q9H8U3 ∙ 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 ZFAND3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFAND3 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in ZFAND3

This is a list of pathogenic ClinVar variants found in the ZFAND3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-37819956-C-A		not specified	Uncertain significance (Aug 17, 2021)
6-37819982-A-T		not specified	Uncertain significance (Dec 15, 2022)
6-38061616-G-A		not specified	Uncertain significance (Jan 11, 2023)
6-38061668-A-G		not specified	Uncertain significance (Aug 04, 2021)
6-38061737-C-T		not specified	Uncertain significance (Mar 11, 2024)
6-38061767-A-G		not specified	Uncertain significance (Dec 22, 2023)
6-38116601-G-A		not specified	Uncertain significance (Mar 14, 2023)
6-38116635-G-A		not specified	Uncertain significance (Feb 06, 2024)
6-38116698-A-G		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFAND3	protein_coding	protein_coding	ENST00000287218	6	335126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.922	0.0782	125714	0	1	125715	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	84	128	0.656	0.00000835	1477
Missense in Polyphen		9	39.882	0.22567		417
Synonymous	-0.129	51	49.8	1.02	0.00000328	429
Loss of Function	3.02	1	12.6	0.0796	7.64e-7	144

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)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.0947
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.237
• hipred: Y
• hipred_score: 0.717
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfand3

Zebrafish Information Network

• Gene name: zfand3
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Molecular function: DNA binding;zinc ion binding