FCHSD1

FCH and double SH3 domains 1, the group of F-BAR domain containing

Basic information

Region (hg38): 5:141639301-141651418

Links

ENSG00000197948 ∙ NCBI:89848 ∙ OMIM:617555 ∙ HGNC:25463 ∙ Uniprot:Q86WN1 ∙ 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 FCHSD1 gene.

• Inborn genetic diseases (44 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCHSD1 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			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8			8
Total	0	0	44	1	0

Variants in FCHSD1

This is a list of pathogenic ClinVar variants found in the FCHSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141639480-A-G		not specified	Uncertain significance (Sep 29, 2022)
5-141639532-C-T		not specified	Uncertain significance (Dec 20, 2023)
5-141639580-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-141639596-G-T		not specified	Uncertain significance (May 23, 2023)
5-141640005-G-T		not specified	Uncertain significance (Aug 13, 2021)
5-141640020-G-A		not specified	Uncertain significance (Dec 17, 2023)
5-141640087-C-A		not specified	Uncertain significance (Sep 13, 2023)
5-141640107-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-141640146-G-A		not specified	Uncertain significance (Nov 08, 2021)
5-141640191-T-C		not specified	Uncertain significance (Jan 18, 2023)
5-141641506-G-C		not specified	Uncertain significance (Jul 12, 2023)
5-141641509-G-A		not specified	Uncertain significance (Feb 06, 2024)
5-141641544-G-A		not specified	Uncertain significance (Dec 20, 2021)
5-141641560-G-A		not specified	Uncertain significance (Sep 17, 2021)
5-141641728-C-T		not specified	Uncertain significance (Oct 25, 2023)
5-141643049-C-T		not specified	Uncertain significance (Oct 25, 2023)
5-141644220-G-T		not specified	Uncertain significance (Jul 29, 2023)
5-141644253-G-A		not specified	Uncertain significance (Jan 10, 2023)
5-141644350-G-A			Likely benign (Mar 01, 2023)
5-141644360-C-T		not specified	Uncertain significance (Aug 22, 2023)
5-141644382-A-G		not specified	Uncertain significance (Dec 28, 2023)
5-141644384-C-T		not specified	Uncertain significance (Feb 14, 2023)
5-141644412-A-C		not specified	Uncertain significance (Nov 30, 2022)
5-141644605-T-C		not specified	Uncertain significance (Feb 07, 2023)
5-141644609-G-C		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCHSD1	protein_coding	protein_coding	ENST00000435817	20	12118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-31	0.0000308	123956	5	699	124660	0.00283

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.798	358	403	0.888	0.0000251	4368
Missense in Polyphen		125	132.86	0.94085		1522
Synonymous	1.97	129	161	0.802	0.00000913	1418
Loss of Function	-0.0655	47	46.5	1.01	0.00000288	447

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00271	0.00268
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.00167	0.00167
Finnish	0.0136	0.0116
European (Non-Finnish)	0.00311	0.00267
Middle Eastern	0.00167	0.00167
South Asian	0.00184	0.00147
Other	0.00285	0.00231

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0882

Intolerance Scores

• loftool: 0.949
• rvis_EVS: 0.23
• rvis_percentile_EVS: 68.54

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.170
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.541

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fchsd1

Gene ontology

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