FREM1
Basic information
Region (hg38): 9:14737151-14910995
Previous symbols: [ "C9orf154" ]
Links
Phenotypes
GenCC
Source:
- oculotrichoanal syndrome (Definitive), mode of inheritance: AR
- trigonocephaly 2 (Disputed Evidence), mode of inheritance: AD
- trigonocephaly 2 (Limited), mode of inheritance: AD
- oculotrichoanal syndrome (Moderate), mode of inheritance: AR
- oculotrichoanal syndrome (Supportive), mode of inheritance: AR
- isolated trigonocephaly (Supportive), mode of inheritance: AD
- renal agenesis, unilateral (Supportive), mode of inheritance: AD
- BNAR syndrome (Supportive), mode of inheritance: AR
- BNAR syndrome (Strong), mode of inheritance: AR
- oculotrichoanal syndrome (Strong), mode of inheritance: AR
- trigonocephaly 2 (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Bifid nose with or without anorectal and renal anomalies; Trigonocephaly 2; Manitoba oculotrichoanal syndrome | AD/AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Dermatologic; Gastrointestinal; Musculoskeletal; Ophthalmologic; Renal | 1554017; 11332973; 11822703; 17352387; 19732862; 21507892; 21931569; 23112756; 23221805 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (496 variants)
- Oculotrichoanal syndrome (224 variants)
- Inborn genetic diseases (117 variants)
- not specified (30 variants)
- BNAR syndrome;Oculotrichoanal syndrome;Trigonocephaly 2 (23 variants)
- Oculotrichoanal syndrome;BNAR syndrome;Trigonocephaly 2 (14 variants)
- Oculotrichoanal syndrome;Trigonocephaly 2;BNAR syndrome (12 variants)
- FREM1-related condition (11 variants)
- Trigonocephaly 2;Oculotrichoanal syndrome;BNAR syndrome (7 variants)
- Trigonocephaly 2 (7 variants)
- BNAR syndrome (6 variants)
- BNAR syndrome;Trigonocephaly 2;Oculotrichoanal syndrome (6 variants)
- Trigonocephaly 2;BNAR syndrome;Oculotrichoanal syndrome (3 variants)
- Congenital diaphragmatic hernia (1 variants)
- Chronic kidney disease (1 variants)
- Congenital anomaly of kidney and urinary tract (1 variants)
- Irido-corneo-trabecular dysgenesis;Rieger anomaly (1 variants)
- Trigonocephaly (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FREM1 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 | 20 | 84 | 26 | 130 | ||
missense | 284 | 20 | 20 | 326 | ||
nonsense | 9 | |||||
start loss | 1 | |||||
frameshift | 7 | |||||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 9 | |||||
splice region ? | 1 | 16 | 9 | 6 | 32 | |
non coding ? | 27 | 32 | 70 | 129 | ||
Total | 11 | 15 | 336 | 136 | 117 |
Highest pathogenic variant AF is 0.000138
Variants in FREM1
This is a list of pathogenic ClinVar variants found in the FREM1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
9-14737156-T-A | Oculotrichoanal syndrome | Uncertain significance (Jan 12, 2018) | ||
9-14737167-G-A | Oculotrichoanal syndrome | Uncertain significance (Jan 12, 2018) | ||
9-14737179-A-C | Oculotrichoanal syndrome | Uncertain significance (Jan 12, 2018) | ||
9-14737194-C-G | Oculotrichoanal syndrome | Likely benign (Jan 13, 2018) | ||
9-14737248-T-C | Oculotrichoanal syndrome | Benign (May 12, 2021) | ||
9-14737256-AT-A | Oculotrichoanal syndrome | Uncertain significance (Jun 14, 2016) | ||
9-14737341-C-A | Oculotrichoanal syndrome | Uncertain significance (Jan 13, 2018) | ||
9-14737386-T-A | Oculotrichoanal syndrome | Uncertain significance (Jan 12, 2018) | ||
9-14737408-G-A | Oculotrichoanal syndrome | Benign/Likely benign (Sep 19, 2023) | ||
9-14737424-T-C | Uncertain significance (Jul 21, 2022) | |||
9-14737454-T-A | Uncertain significance (Jun 09, 2022) | |||
9-14737462-C-T | FREM1-related disorder | Benign/Likely benign (Jan 26, 2024) | ||
9-14737471-T-C | Oculotrichoanal syndrome | Conflicting classifications of pathogenicity (Dec 21, 2023) | ||
9-14737482-C-T | Oculotrichoanal syndrome • Oculotrichoanal syndrome;BNAR syndrome;Trigonocephaly 2 | Uncertain significance (Mar 23, 2022) | ||
9-14737490-T-C | Inborn genetic diseases | Uncertain significance (Mar 06, 2023) | ||
9-14737505-C-T | Uncertain significance (Nov 10, 2022) | |||
9-14737506-G-A | Oculotrichoanal syndrome;BNAR syndrome;Trigonocephaly 2 | Uncertain significance (Dec 29, 2021) | ||
9-14737508-T-G | not specified • Oculotrichoanal syndrome | Benign (Jan 31, 2024) | ||
9-14737518-C-T | Uncertain significance (Dec 23, 2021) | |||
9-14737528-A-G | Likely benign (Mar 22, 2023) | |||
9-14737544-G-A | Inborn genetic diseases | Uncertain significance (Jan 09, 2024) | ||
9-14737573-A-G | Oculotrichoanal syndrome | Uncertain significance (Mar 02, 2018) | ||
9-14737577-T-A | Inborn genetic diseases | Uncertain significance (Dec 03, 2021) | ||
9-14737577-T-C | Uncertain significance (Oct 22, 2023) | |||
9-14737588-G-A | FREM1-related disorder | Likely benign (Mar 25, 2019) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FREM1 | protein_coding | protein_coding | ENST00000422223 | 36 | 176330 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.57e-52 | 2.53e-7 | 124467 | 1 | 211 | 124679 | 0.000851 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -3.51 | 1485 | 1.15e+3 | 1.29 | 0.0000597 | 14317 |
Missense in Polyphen | 346 | 286.77 | 1.2065 | 3704 | ||
Synonymous | -5.00 | 575 | 441 | 1.30 | 0.0000246 | 4182 |
Loss of Function | 0.608 | 83 | 89.2 | 0.931 | 0.00000428 | 1126 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00244 | 0.00234 |
Ashkenazi Jewish | 0.000301 | 0.000298 |
East Asian | 0.000572 | 0.000556 |
Finnish | 0.000704 | 0.000696 |
European (Non-Finnish) | 0.000717 | 0.000699 |
Middle Eastern | 0.000572 | 0.000556 |
South Asian | 0.00168 | 0.00160 |
Other | 0.000501 | 0.000495 |
dbNSFP
Source:
- Function
- FUNCTION: Extracellular matrix protein that plays a role in epidermal differentiation and is required for epidermal adhesion during embryonic development. {ECO:0000250}.;
- Disease
- DISEASE: Bifid nose, with or without anorectal and renal anomalies (BNAR) [MIM:608980]: A disease characterized by the presence of a bifid nose usually associated with renal agenesis and anorectal malformations. A bifid nose is a congenital deformity due to failure of the paired nasal processes to fuse to a single midline organ during early gestation. {ECO:0000269|PubMed:19732862}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Manitoba oculotrichoanal syndrome (MOTA) [MIM:248450]: A rare condition defined by eyelid colobomas, cryptophthalmos, and anophthalmia/microphthalmia, an aberrant hairline, a bifid or broad nasal tip, and gastrointestinal anomalies such as omphalocele and anal stenosis. {ECO:0000269|PubMed:21507892, ECO:0000269|PubMed:28111185}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Trigonocephaly 2 (TRIGNO2) [MIM:614485]: A keel-shaped deformation of the forehead, caused by premature fusion of the metopic sutures. It results in a triangular shape of the head. {ECO:0000269|PubMed:21931569}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- 0.995
- rvis_EVS
- -0.63
- rvis_percentile_EVS
- 17.04
Haploinsufficiency Scores
- pHI
- 0.100
- hipred
- hipred_score
- ghis
- 0.471
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.548
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | Medium | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Frem1
- Phenotype
- liver/biliary system phenotype; respiratory system phenotype; reproductive system phenotype; normal 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); vision/eye phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype; endocrine/exocrine gland 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); growth/size/body region phenotype; craniofacial phenotype; muscle phenotype;
Zebrafish Information Network
- Gene name
- frem1a
- Affected structure
- dorsal fin
- Phenotype tag
- abnormal
- Phenotype quality
- has fewer parts of type
Gene ontology
- Biological process
- cell communication;cell-matrix adhesion;craniofacial suture morphogenesis
- Cellular component
- basement membrane;integral component of membrane
- Molecular function
- carbohydrate binding;metal ion binding