FLYWCH2

FLYWCH family member 2

Basic information

Region (hg38): 16:2883213-2899382

Links

ENSG00000162076 ∙ NCBI:114984 ∙ ∙ HGNC:25178 ∙ Uniprot:Q96CP2 ∙ 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 FLYWCH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FLYWCH2 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in FLYWCH2

This is a list of pathogenic ClinVar variants found in the FLYWCH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2896462-G-A		not specified	Uncertain significance (Nov 25, 2024)
16-2896526-C-G		not specified	Uncertain significance (Oct 03, 2023)
16-2896538-C-T		not specified	Uncertain significance (Jun 13, 2024)
16-2896663-G-A		not specified	Uncertain significance (Mar 02, 2023)
16-2896753-C-T		not specified	Uncertain significance (Mar 06, 2023)
16-2899070-G-A		not specified	Uncertain significance (Dec 17, 2023)
16-2899082-C-T		not specified	Uncertain significance (Nov 14, 2023)
16-2899130-C-T		not specified	Uncertain significance (Dec 01, 2022)
16-2899135-G-A		not specified	Likely benign (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FLYWCH2	protein_coding	protein_coding	ENST00000396958	2	16197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.187	0.658	125618	0	4	125622	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0901	88	85.7	1.03	0.00000496	880
Missense in Polyphen		30	29.952	1.0016		306
Synonymous	-2.04	54	38.0	1.42	0.00000231	307
Loss of Function	0.919	1	2.60	0.385	1.09e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000698	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.273
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.0639
• hipred: N
• hipred_score: 0.112
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0572

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Flywch2

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: RNA binding