ZFR

zinc finger RNA binding protein, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 5:32354350-32444740

Links

ENSG00000056097 ∙ NCBI:51663 ∙ OMIM:615635 ∙ HGNC:17277 ∙ Uniprot:Q96KR1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive spastic paraplegia type 71 (Supportive), mode of inheritance: AR
• hereditary spastic paraplegia (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZFR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFR 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				58	3	61
missense			94	2	2	98
nonsense						0
start loss						0
frameshift						0
inframe indel			6			6
splice donor/acceptor (+/-2bp)						0
splice region			3	13	1	17
non coding			2	29	5	36
Total	0	0	102	89	10

Variants in ZFR

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

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

Position	Type	Phenotype	Significance	ClinVar
5-32355774-A-G		Pure or complex autosomal recessive spastic paraplegia	Uncertain significance (Sep 23, 2024)
5-32355826-A-G		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Nov 05, 2024)
5-32355844-G-A		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Aug 01, 2024)
5-32355871-C-T		Pure or complex autosomal recessive spastic paraplegia • not specified	Uncertain significance (Dec 23, 2024)
5-32355873-T-C		Pure or complex autosomal recessive spastic paraplegia • not specified	Uncertain significance (Jan 15, 2023)
5-32355877-C-A		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Sep 05, 2024)
5-32355877-C-T		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Jun 23, 2023)
5-32355878-G-A		Pure or complex autosomal recessive spastic paraplegia	Uncertain significance (Jul 09, 2022)
5-32355879-G-T		Pure or complex autosomal recessive spastic paraplegia	Uncertain significance (Feb 24, 2024)
5-32355890-A-G		Pure or complex autosomal recessive spastic paraplegia	Uncertain significance (Aug 04, 2023)
5-32355909-T-C		Pure or complex autosomal recessive spastic paraplegia • not specified	Uncertain significance (Sep 15, 2023)
5-32355923-A-C		Pure or complex autosomal recessive spastic paraplegia	Uncertain significance (Sep 28, 2024)
5-32355925-G-A		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Jun 03, 2022)
5-32355946-CAA-C		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Mar 11, 2024)
5-32355948-AAG-A		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Feb 24, 2024)
5-32355959-A-T		Pure or complex autosomal recessive spastic paraplegia	Likely benign (May 01, 2022)
5-32363939-T-C		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Dec 24, 2021)
5-32363954-A-T		not specified	Uncertain significance (Sep 03, 2024)
5-32363959-A-T		not specified	Uncertain significance (Aug 14, 2024)
5-32363963-G-A		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Mar 10, 2021)
5-32363973-C-T			Uncertain significance (Feb 21, 2024)
5-32363987-C-T		not specified	Uncertain significance (Oct 06, 2021)
5-32364012-T-A		Pure or complex autosomal recessive spastic paraplegia	Uncertain significance (Aug 11, 2022)
5-32364030-A-G		Pure or complex autosomal recessive spastic paraplegia	Uncertain significance (Apr 05, 2023)
5-32364049-C-T		Pure or complex autosomal recessive spastic paraplegia	Likely benign (Jun 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFR	protein_coding	protein_coding	ENST00000265069	20	90412

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.35e-8	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.09	303	580	0.522	0.0000308	6924
Missense in Polyphen		14	46.461	0.30133		548
Synonymous	0.257	200	205	0.977	0.0000109	2159
Loss of Function	6.87	3	60.8	0.0493	0.00000364	673

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000356	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in postimplantation and gastrulation stages of development. Involved in the nucleocytoplasmic shuttling of STAU2. Binds to DNA and RNA (By similarity). {ECO:0000250}.
• Pathway: Exercise-induced Circadian Regulation (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.0979
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.638
• hipred: Y
• hipred_score: 0.717
• ghis: 0.674

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• 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: Zfr
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: multicellular organism development
• Cellular component: nucleus;chromosome;cytoplasm
• Molecular function: DNA binding;RNA binding;double-stranded RNA binding;single-stranded RNA binding;protein binding;zinc ion binding