GeneBe

FRMD7

FERM domain containing 7, the group of FERM domain containing

Basic information

Region (hg38): X:132076990-132128020

Previous symbols: [ "NYS", "NYS1" ]

Links

ENSG00000165694 ∙ NCBI:90167 ∙ OMIM:300628 ∙ HGNC:8079 ∙ Uniprot:Q6ZUT3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • nystagmus 1, congenital, X-linked (Definitive), mode of inheritance: XL
  • nystagmus 1, congenital, X-linked (Strong), mode of inheritance: XL
  • nystagmus 1, congenital, X-linked (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Nystagmus 1, congenital, X-linkedXLGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic16020310; 16240070; 17013395; 18087240; 17768376; 19072571; 17962394; 21746984; 21303855; 21386928; 21746984; 22065930; 22262942; 22490987

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FRMD7 gene.

  • not_provided (382 variants)
  • Inborn_genetic_diseases (65 variants)
  • Nystagmus_1,_congenital,_X-linked (50 variants)
  • FRMD7-related_disorder (4 variants)
  • not_specified (3 variants)
  • Retinal_dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRMD7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000194277.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
6
clinvar
50
clinvar
14
clinvar
 71
missense
7
clinvar
11
clinvar
202
clinvar
36
clinvar
9
clinvar
 265
nonsense
10
clinvar
2
clinvar
1
clinvar
 13
start loss
3
 3
frameshift
9
clinvar
3
clinvar
1
clinvar
 13
splice donor/acceptor (+/-2bp)
5
clinvar
5
clinvar
1
clinvar
 11
Total 35 21 210 86 24

Highest pathogenic variant AF is 0.000114164315

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FRMD7protein_codingprotein_codingENST00000298542 1251028
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.7300.270125613251256200.0000279
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7042252570.8760.00001844753
Missense in Polyphen79109.960.718422091
Synonymous0.2589093.20.9660.000006631321
Loss of Function3.54421.80.1830.00000163402

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00007290.0000729
Ashkenazi Jewish0.000.00
East Asian0.00007230.0000544
Finnish0.000.00
European (Non-Finnish)0.00003680.0000264
Middle Eastern0.00007230.0000544
South Asian0.000.00
Other0.0002220.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in neurite development, may be through the activation of the GTPase RAC1. Plays a role in the control of eye movement and gaze stability. {ECO:0000250|UniProtKB:A2AD83, ECO:0000269|PubMed:17013395, ECO:0000269|PubMed:23946638}.;
Disease
DISEASE: Nystagmus congenital X-linked 1 (NYS1) [MIM:310700]: A condition defined as conjugated, spontaneous and involuntary ocular oscillations that appear at birth or during the first three months of life. Other associated features may include mildly decreased visual acuity, strabismus, astigmatism, and occasionally head nodding. {ECO:0000269|PubMed:17013395, ECO:0000269|PubMed:17397053, ECO:0000269|PubMed:17768376, ECO:0000269|PubMed:17893669, ECO:0000269|PubMed:17962394, ECO:0000269|PubMed:18087240, ECO:0000269|PubMed:18246032, ECO:0000269|PubMed:18431453, ECO:0000269|PubMed:21303855, ECO:0000269|PubMed:21365021, ECO:0000269|PubMed:22490987, ECO:0000269|PubMed:23946638}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.124

Intolerance Scores

loftool
0.107
rvis_EVS
0.31
rvis_percentile_EVS
72.38

Haploinsufficiency Scores

pHI
0.153
hipred
Y
hipred_score
0.521
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.181

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Frmd7
Phenotype
skeleton phenotype;

Gene ontology

Biological process
positive regulation of lamellipodium assembly;regulation of neuron projection development;negative regulation of protein binding;positive regulation of small GTPase mediated signal transduction;negative regulation of stress fiber assembly
Cellular component
extracellular space;cytoskeleton;growth cone;neuron projection;neuronal cell body
Molecular function
molecular_function