FCHSD2

FCH and double SH3 domains 2, the group of F-BAR domain containing

Basic information

Region (hg38): 11:72836744-73142318

Previous symbols: [ "SH3MD3" ]

Links

ENSG00000137478 ∙ NCBI:9873 ∙ OMIM:617556 ∙ HGNC:29114 ∙ Uniprot:O94868 ∙ 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 FCHSD2 gene.

• Inborn genetic diseases (27 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCHSD2 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					1	1
missense			27		1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	27	0	2

Variants in FCHSD2

This is a list of pathogenic ClinVar variants found in the FCHSD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-72838819-A-G		not specified	Uncertain significance (Sep 17, 2021)
11-72838859-G-C		not specified	Uncertain significance (Feb 06, 2023)
11-72840888-T-G		not specified	Uncertain significance (Mar 01, 2023)
11-72840947-T-A		not specified	Uncertain significance (Jun 21, 2022)
11-72841471-C-G		not specified	Uncertain significance (Aug 04, 2023)
11-72841540-G-A			Benign (Jul 23, 2018)
11-72842708-A-T		not specified	Uncertain significance (Jan 17, 2023)
11-72842718-C-G		not specified	Uncertain significance (Sep 21, 2023)
11-72843181-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-72843280-G-T		not specified	Uncertain significance (May 05, 2023)
11-72849829-C-T		not specified	Uncertain significance (Nov 03, 2023)
11-72849830-G-T		not specified	Uncertain significance (Oct 27, 2022)
11-72849840-A-G		not specified	Uncertain significance (Dec 12, 2023)
11-72849863-T-G		not specified	Uncertain significance (Aug 02, 2021)
11-72849864-T-C		not specified	Uncertain significance (Aug 02, 2021)
11-72849874-C-T		not specified	Uncertain significance (Jan 08, 2024)
11-72867866-G-A		not specified	Uncertain significance (Oct 24, 2023)
11-72867911-C-T		not specified	Uncertain significance (Nov 12, 2021)
11-72867945-T-C		not specified	Uncertain significance (Aug 01, 2022)
11-72867983-T-C		not specified	Uncertain significance (Nov 17, 2022)
11-72868001-C-T		not specified	Uncertain significance (Dec 07, 2021)
11-72868021-A-G			Benign (Dec 14, 2017)
11-72868025-A-G		not specified	Uncertain significance (May 16, 2022)
11-72887547-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-72887555-C-A		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCHSD2	protein_coding	protein_coding	ENST00000409418	20	305517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.566	0.434	125577	0	16	125593	0.0000637

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.84	289	392	0.738	0.0000212	4839
Missense in Polyphen		68	130.57	0.52079		1750
Synonymous	0.424	134	140	0.954	0.00000758	1341
Loss of Function	4.95	10	46.4	0.216	0.00000252	548

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000110	0.000106
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.846
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.37

Haploinsufficiency Scores

• pHI: 0.400
• hipred: Y
• hipred_score: 0.595
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fchsd2

Gene ontology

• Biological process: neuromuscular synaptic transmission;regulation of actin filament polymerization
• Cellular component: neuromuscular junction;recycling endosome
• Molecular function: protein binding