FOXS1

forkhead box S1, the group of Forkhead boxes

Basic information

Region (hg38): 20:31844303-31845604

Previous symbols: [ "FKHL18" ]

Links

ENSG00000179772 ∙ NCBI:2307 ∙ OMIM:602939 ∙ HGNC:3735 ∙ Uniprot:O43638 ∙ 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 FOXS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXS1 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			34	4		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	4	0

Variants in FOXS1

This is a list of pathogenic ClinVar variants found in the FOXS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-31844575-G-A		not specified	Uncertain significance (Nov 15, 2024)
20-31844612-C-T		not specified	Likely benign (May 30, 2024)
20-31844660-G-C		not specified	Uncertain significance (Apr 22, 2024)
20-31844683-G-T		not specified	Uncertain significance (Dec 21, 2023)
20-31844695-C-T		not specified	Uncertain significance (Nov 08, 2024)
20-31844768-T-A		not specified	Uncertain significance (Feb 03, 2025)
20-31844792-G-A		not specified	Uncertain significance (Oct 27, 2023)
20-31844810-C-T		not specified	Uncertain significance (Dec 01, 2023)
20-31844824-G-A		not specified	Uncertain significance (Aug 01, 2024)
20-31844831-A-T		not specified	Uncertain significance (Jan 01, 2025)
20-31844861-C-T		not specified	Uncertain significance (Nov 07, 2024)
20-31844876-C-T		not specified	Uncertain significance (Jul 20, 2021)
20-31844921-C-T		not specified	Uncertain significance (Sep 03, 2024)
20-31844923-G-T		not specified	Uncertain significance (Apr 12, 2022)
20-31844953-G-A		not specified	Uncertain significance (Jun 29, 2023)
20-31844974-A-G		not specified	Likely benign (Sep 20, 2024)
20-31844983-C-T		not specified	Likely benign (Dec 21, 2022)
20-31844989-C-A		not specified	Uncertain significance (Mar 01, 2024)
20-31845029-C-T		not specified	Uncertain significance (Mar 08, 2024)
20-31845065-C-G		not specified	Uncertain significance (Oct 12, 2022)
20-31845074-C-G		not specified	Uncertain significance (Mar 07, 2023)
20-31845093-C-A		not specified	Uncertain significance (Dec 17, 2024)
20-31845136-G-A		not specified	Uncertain significance (Jan 18, 2023)
20-31845152-G-A		not specified	Uncertain significance (Dec 17, 2023)
20-31845158-C-T		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXS1	protein_coding	protein_coding	ENST00000375978	1	1318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.233	0.737	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.434	205	223	0.918	0.0000154	2098
Missense in Polyphen		87	104.47	0.83275		991
Synonymous	0.816	83	93.0	0.892	0.00000605	740
Loss of Function	1.82	2	7.29	0.274	3.99e-7	84

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that suppresses transcription from the FASLG, FOXO3 and FOXO4 promoters. May have a role in the organization of the testicular vasculature (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.137
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.0888
• hipred: N
• hipred_score: 0.146
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxs1
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;blood vessel development;regulation of transcription by RNA polymerase II;anatomical structure morphogenesis;cell differentiation;positive regulation of multicellular organism growth;negative regulation of DNA-binding transcription factor activity;negative regulation of transcription, DNA-templated;neuromuscular process controlling balance
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity