FMN1
Basic information
Region (hg38): 15:32765544-33194714
Previous symbols: [ "LD", "FMN" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FMN1 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 | 14 | 38 | 21 | 73 | ||
missense | 145 | 28 | 33 | 206 | ||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 6 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 5 | 5 | ||||
non coding | 12 | 75 | 89 | |||
Total | 0 | 0 | 167 | 79 | 131 |
Variants in FMN1
This is a list of pathogenic ClinVar variants found in the FMN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-32774126-G-A | Benign (May 12, 2021) | |||
15-32774277-C-T | Benign (May 12, 2021) | |||
15-32774309-C-T | not specified • FMN1-related disorder | Likely benign (Feb 10, 2015) | ||
15-32774324-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
15-32774325-A-C | Likely benign (Dec 07, 2022) | |||
15-32774341-C-T | not specified | Uncertain significance (Aug 28, 2023) | ||
15-32774363-G-GA | Likely benign (Jun 12, 2023) | |||
15-32774368-A-G | Likely benign (Oct 31, 2022) | |||
15-32774381-T-A | Benign (May 12, 2021) | |||
15-32774521-CCCTA-C | Benign (May 12, 2021) | |||
15-32776687-CT-C | Benign (May 11, 2021) | |||
15-32776688-T-TTC | Benign (May 13, 2021) | |||
15-32776826-A-G | Benign (Oct 05, 2023) | |||
15-32776918-A-G | Likely benign (Dec 06, 2022) | |||
15-32777103-G-A | Benign (May 12, 2021) | |||
15-32798683-T-G | Benign (May 12, 2021) | |||
15-32798813-G-C | not specified | Uncertain significance (Mar 25, 2022) | ||
15-32798832-G-C | not specified | Uncertain significance (Jan 10, 2022) | ||
15-32798867-T-C | FMN1-related disorder | Uncertain significance (May 31, 2024) | ||
15-32798875-C-T | Uncertain significance (Jul 25, 2022) | |||
15-32798878-A-G | Benign (Jan 29, 2024) | |||
15-32798883-C-A | Uncertain significance (Dec 01, 2021) | |||
15-32798883-C-T | not specified • FMN1-related disorder | Likely benign (Jul 13, 2022) | ||
15-32798901-CCTT-C | not specified | Benign (Jan 29, 2024) | ||
15-32798934-A-G | Uncertain significance (Sep 19, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FMN1 | protein_coding | protein_coding | ENST00000334528 | 17 | 429151 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.59e-18 | 0.635 | 124478 | 0 | 177 | 124655 | 0.000710 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.53 | 721 | 614 | 1.17 | 0.0000323 | 7769 |
Missense in Polyphen | 111 | 138.21 | 0.80315 | 1867 | ||
Synonymous | -3.43 | 306 | 239 | 1.28 | 0.0000135 | 2316 |
Loss of Function | 1.93 | 35 | 49.7 | 0.704 | 0.00000253 | 664 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00210 | 0.00209 |
Ashkenazi Jewish | 0.000309 | 0.000298 |
East Asian | 0.000955 | 0.000946 |
Finnish | 0.000613 | 0.000603 |
European (Non-Finnish) | 0.000609 | 0.000584 |
Middle Eastern | 0.000955 | 0.000946 |
South Asian | 0.000893 | 0.000883 |
Other | 0.000331 | 0.000330 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the formation of adherens junction and the polymerization of linear actin cables. {ECO:0000250}.;
- Pathway
- E-cadherin signaling in keratinocytes
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.991
- rvis_EVS
- 0.86
- rvis_percentile_EVS
- 88.64
Haploinsufficiency Scores
- pHI
- 0.272
- hipred
- N
- hipred_score
- 0.222
- ghis
- 0.433
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.670
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Fmn1
- Phenotype
- skeleton phenotype; renal/urinary system phenotype; limbs/digits/tail phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; pigmentation phenotype; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- gene expression;forelimb morphogenesis;hindlimb morphogenesis;actin nucleation;skeletal system morphogenesis;positive regulation of actin nucleation;positive regulation of focal adhesion assembly;ureteric bud invasion
- Cellular component
- nucleus;cytoplasm;actin filament;plasma membrane;adherens junction
- Molecular function
- actin binding;microtubule binding;SH3 domain binding