FHL3

four and a half LIM domains 3, the group of LIM domain containing

Basic information

Region (hg38): 1:37996769-38005606

Links

ENSG00000183386 ∙ NCBI:2275 ∙ OMIM:602790 ∙ HGNC:3704 ∙ Uniprot:Q13643 ∙ 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 FHL3 gene.

• Inborn genetic diseases (15 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FHL3 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				3		3
missense			14	1	1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	1

Variants in FHL3

This is a list of pathogenic ClinVar variants found in the FHL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-37997454-G-A		not specified	Uncertain significance (Jun 03, 2022)
1-37997459-G-A			Likely benign (Sep 01, 2022)
1-37997478-G-C		not specified	Uncertain significance (May 26, 2023)
1-37997484-G-C		not specified	Uncertain significance (Oct 18, 2021)
1-37997494-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-37997524-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-37997720-C-G		not specified	Uncertain significance (Jan 03, 2024)
1-37997820-T-A		not specified	Uncertain significance (Jul 06, 2022)
1-37997859-C-G		not specified	Uncertain significance (Jun 27, 2022)
1-37997971-A-C		not specified	Uncertain significance (Nov 03, 2022)
1-37998026-A-T			Likely benign (Mar 01, 2022)
1-37998027-C-A		not specified	Uncertain significance (May 24, 2023)
1-37998048-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-37998058-G-C		not specified	Uncertain significance (Jul 12, 2023)
1-37998102-G-A		not specified	Uncertain significance (May 23, 2023)
1-37998115-A-G		not specified	Uncertain significance (Aug 13, 2021)
1-37998126-C-T		not specified	Uncertain significance (Mar 02, 2023)
1-37998996-A-G			Likely benign (Mar 01, 2022)
1-37998998-C-T			Benign (Nov 20, 2018)
1-37999088-G-A		not specified	Uncertain significance (Mar 29, 2022)
1-37999277-G-A		not specified	Uncertain significance (Dec 12, 2023)
1-37999316-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-37999366-C-A		not specified	Uncertain significance (Aug 23, 2021)
1-37999379-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-37999381-T-C		not specified	Likely benign (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FHL3	protein_coding	protein_coding	ENST00000373016	5	8837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00178	0.976	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.793	153	183	0.835	0.0000118	1831
Missense in Polyphen		65	88.328	0.7359		875
Synonymous	0.347	70	73.8	0.949	0.00000483	520
Loss of Function	2.01	7	15.6	0.450	8.13e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.193
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• pHI: 0.298
• hipred: Y
• hipred_score: 0.825
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.710

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fhl3

Gene ontology

• Biological process: muscle organ development;actin cytoskeleton organization
• Cellular component: stress fiber;nucleus;focal adhesion;Z disc
• Molecular function: actin binding;protein binding;metal ion binding