ZFAND2B

zinc finger AN1-type containing 2B, the group of Zinc fingers AN1-type

Basic information

Region (hg38): 2:219195237-219209651

Links

ENSG00000158552 ∙ NCBI:130617 ∙ OMIM:613474 ∙ HGNC:25206 ∙ Uniprot:Q8WV99 ∙ 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 ZFAND2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFAND2B 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			21	2		23
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	2	0

Variants in ZFAND2B

This is a list of pathogenic ClinVar variants found in the ZFAND2B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219207332-C-A		not specified	Uncertain significance (Mar 07, 2023)
2-219207687-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-219207742-G-C		not specified	Uncertain significance (Dec 09, 2024)
2-219207759-C-T		not specified	Uncertain significance (Aug 21, 2023)
2-219207769-A-G		not specified	Uncertain significance (Mar 20, 2024)
2-219207775-G-A		not specified	Uncertain significance (Jun 27, 2022)
2-219207897-A-G		not specified	Uncertain significance (Sep 27, 2021)
2-219207908-C-T		not specified	Uncertain significance (Apr 25, 2023)
2-219207921-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-219207962-C-G		not specified	Uncertain significance (Feb 23, 2023)
2-219208031-C-T		not specified	Uncertain significance (Jul 26, 2021)
2-219208268-C-G		not specified	Uncertain significance (Oct 30, 2024)
2-219208291-C-T		not specified	Uncertain significance (Sep 08, 2024)
2-219208308-A-G		not specified	Uncertain significance (May 25, 2022)
2-219208593-C-T		not specified	Uncertain significance (Aug 28, 2023)
2-219208597-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-219208609-C-T		not specified	Uncertain significance (Dec 28, 2023)
2-219208620-A-G		not specified	Uncertain significance (Oct 22, 2024)
2-219209039-A-G		not specified	Likely benign (Oct 12, 2021)
2-219209042-G-A		not specified	Likely benign (Aug 09, 2021)
2-219209269-G-A		not specified	Uncertain significance (Nov 14, 2023)
2-219209272-G-A		not specified	Uncertain significance (Sep 15, 2021)
2-219209274-A-C		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFAND2B	protein_coding	protein_coding	ENST00000289528	9	14415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000248	0.926	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.342	142	154	0.922	0.00000888	1669
Missense in Polyphen		54	75.617	0.71413		836
Synonymous	0.248	53	55.3	0.958	0.00000288	502
Loss of Function	1.66	10	17.5	0.571	0.00000102	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in protein homeostasis by regulating both the translocation and the ubiquitin-mediated proteasomal degradation of nascent proteins at the endoplasmic reticulum. It is involved in the regulation of signal-mediated translocation of proteins into the endoplasmic reticulum. It also plays a role in the ubiquitin-mediated proteasomal degradation of proteins for which signal-mediated translocation to the endoplasmic reticulum has failed. May therefore function in the endoplasmic reticulum stress-induced pre-emptive quality control, a mechanism that selectively attenuates the translocation of newly synthesized proteins into the endoplasmic reticulum and reroutes them to the cytosol for proteasomal degradation (By similarity). By controlling the steady-state expression of the IGF1R receptor, indirectly regulates the insulin-like growth factor receptor signaling pathway (PubMed:26692333). {ECO:0000250|UniProtKB:Q91X58, ECO:0000269|PubMed:26692333}.

Recessive Scores

• pRec: 0.0847

Intolerance Scores

• loftool: 0.720
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.218
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfand2b

Gene ontology

• Biological process: SRP-dependent cotranslational protein targeting to membrane, translocation;proteasome-mediated ubiquitin-dependent protein catabolic process;regulation of insulin-like growth factor receptor signaling pathway;protein targeting to ER
• Cellular component: proteasome complex;endoplasmic reticulum;endoplasmic reticulum membrane;anchored component of membrane
• Molecular function: protein binding;zinc ion binding;K48-linked polyubiquitin modification-dependent protein binding;ubiquitin binding