FLYWCH1

FLYWCH-type zinc finger 1, the group of Zinc fingers

Basic information

Region (hg38): 16:2911931-2951208

Links

ENSG00000059122 ∙ NCBI:84256 ∙ ∙ HGNC:25404 ∙ Uniprot:Q4VC44 ∙ 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 FLYWCH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FLYWCH1 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				6	2	8
missense			121	9	2	132
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	121	15	4

Variants in FLYWCH1

This is a list of pathogenic ClinVar variants found in the FLYWCH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2929698-G-A		not specified	Uncertain significance (Mar 28, 2024)
16-2929707-G-C		not specified	Uncertain significance (Aug 26, 2024)
16-2929717-G-A		not specified	Uncertain significance (Aug 14, 2024)
16-2929731-G-T		not specified	Uncertain significance (Oct 26, 2022)
16-2929734-G-A		not specified	Uncertain significance (Feb 28, 2023)
16-2929762-C-T		not specified	Uncertain significance (Jan 26, 2023)
16-2929766-C-A		not specified	Uncertain significance (Oct 03, 2023)
16-2929793-C-G			Likely benign (May 01, 2022)
16-2929797-G-A		not specified	Likely benign (Nov 09, 2021)
16-2929821-A-G		not specified	Uncertain significance (Mar 30, 2024)
16-2929833-C-G		not specified	Likely benign (Mar 15, 2024)
16-2929878-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-2929887-C-A		not specified	Uncertain significance (Jun 27, 2023)
16-2929905-G-A		not specified	Uncertain significance (May 17, 2023)
16-2929906-C-G		not specified	Uncertain significance (May 20, 2024)
16-2929911-C-G		not specified	Uncertain significance (Jan 14, 2025)
16-2929997-C-A		not specified	Uncertain significance (Oct 30, 2023)
16-2930000-G-C		not specified	Uncertain significance (Sep 25, 2024)
16-2930005-A-G			Likely benign (Dec 01, 2022)
16-2930416-C-G		not specified	Uncertain significance (Dec 07, 2024)
16-2930430-T-C		not specified	Uncertain significance (Apr 06, 2022)
16-2930436-A-G		not specified	Uncertain significance (Sep 22, 2023)
16-2930437-G-C		not specified	Uncertain significance (Jan 24, 2025)
16-2930455-G-A		not specified	Uncertain significance (Nov 07, 2022)
16-2930486-G-C		not specified	Uncertain significance (Mar 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FLYWCH1	protein_coding	protein_coding	ENST00000416288	8	39272

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.67e-19	0.00421	125303	0	247	125550	0.000984

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.61	606	450	1.35	0.0000322	4451
Missense in Polyphen		172	126.78	1.3567		1191
Synonymous	-5.20	284	192	1.48	0.0000130	1484
Loss of Function	0.0761	28	28.4	0.985	0.00000169	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.000943
Ashkenazi Jewish	0.0136	0.0136
East Asian	0.000833	0.000707
Finnish	0.000515	0.000509
European (Non-Finnish)	0.000328	0.000309
Middle Eastern	0.000833	0.000707
South Asian	0.000544	0.000523
Other	0.00250	0.00245

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.159
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.31

Haploinsufficiency Scores

• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.869

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Flywch1

Gene ontology

• Cellular component: nucleoplasm;cytosol;nuclear body
• Molecular function: DNA binding;metal ion binding