ZGRF1

zinc finger GRF-type containing 1, the group of Zinc fingers GRF-type|UPF1 like RNA helicases

Basic information

Region (hg38): 4:112539333-112636995

Previous symbols: [ "C4orf21" ]

Links

ENSG00000138658 ∙ NCBI:55345 ∙ ∙ HGNC:25654 ∙ Uniprot:Q86YA3 ∙ 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 ZGRF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZGRF1 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			98	6	2	106
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6			6
Total	0	0	106	6	2

Variants in ZGRF1

This is a list of pathogenic ClinVar variants found in the ZGRF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-112539641-T-C		not specified	Uncertain significance (May 12, 2024)
4-112539866-C-T		not specified	Uncertain significance (Dec 04, 2024)
4-112539901-T-C		not specified	Uncertain significance (Jun 02, 2023)
4-112539964-T-C		not specified	Uncertain significance (Jul 19, 2022)
4-112539984-A-C		not specified	Uncertain significance (Jan 08, 2024)
4-112539989-A-C		not specified	Uncertain significance (Aug 10, 2021)
4-112540082-T-C		not specified	Uncertain significance (May 29, 2024)
4-112540117-T-C		not specified	Uncertain significance (Sep 07, 2022)
4-112540915-G-A		not specified	Uncertain significance (Oct 10, 2023)
4-112540939-C-T		not specified	Uncertain significance (Dec 21, 2022)
4-112540943-T-C		not specified	Uncertain significance (Jun 23, 2023)
4-112540954-A-G		not specified	Uncertain significance (Dec 14, 2023)
4-112541153-C-T		not specified	Uncertain significance (Oct 09, 2024)
4-112541235-G-A		not specified	Uncertain significance (Jan 29, 2024)
4-112541256-T-C		not specified	Likely benign (Jan 23, 2024)
4-112541258-G-A		not specified	Uncertain significance (Feb 13, 2024)
4-112547367-T-C		not specified	Uncertain significance (Mar 07, 2024)
4-112547377-C-T		not specified	Uncertain significance (Dec 07, 2021)
4-112548271-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-112548335-T-C		not specified	Uncertain significance (Jan 18, 2022)
4-112548368-C-G		not specified	Uncertain significance (Nov 20, 2024)
4-112553893-T-C		not specified	Uncertain significance (Jan 26, 2022)
4-112554733-T-G		not specified	Uncertain significance (Mar 25, 2024)
4-112554756-A-C		not specified	Uncertain significance (Apr 27, 2022)
4-112558160-C-T		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZGRF1	protein_coding	protein_coding	ENST00000505019	27	97660

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.16e-42	0.000340	125427	0	320	125747	0.00127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.463	971	1.01e+3	0.959	0.0000480	13877
Missense in Polyphen		210	250.42	0.8386		3574
Synonymous	1.14	342	370	0.925	0.0000185	3871
Loss of Function	1.51	73	88.3	0.827	0.00000434	1234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00324	0.00323
Ashkenazi Jewish	0.000904	0.000893
East Asian	0.000914	0.000870
Finnish	0.000993	0.000971
European (Non-Finnish)	0.00101	0.000967
Middle Eastern	0.000914	0.000870
South Asian	0.00222	0.00203
Other	0.00200	0.00196

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0563
• hipred: N
• hipred_score: 0.123
• ghis: 0.541

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Zgrf1

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: RNA binding;zinc ion binding