GeneBe

FRMD7

protein-coding

FERM domain containing 7, the group of FERM domain containing

Gene summary

Predicted to be involved in regulation of neuron projection development. Predicted to act upstream of or within negative regulation of stress fiber assembly; positive regulation of lamellipodium assembly; and positive regulation of small GTPase mediated signal transduction. Located in obsolete extracellular space. Implicated in congenital nystagmus 1. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:
  • NYS
  • NYS1

MANE transcript

NM_194277.3

Inheritance

XL

ClinVar variants

P:78U:277B:122

Top phenotype

Nystagmus 1, congenital, X-linked

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chrX:132,076,990-132,128,020

External References & Databases

Ensembl (ENSG00000165694)NCBI Gene (90167)OMIM (300628)HGNC:8079GenCCUniProt (Q6ZUT3)AlphaFoldClinVar (FRMD7)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~51.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

nystagmus 1, congenital, X-linkedSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010693

Submitter: Labcorp Genetics (formerly Invitae)

nystagmus 1, congenital, X-linkedDEFINITIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010693

Submitter: Ambry Genetics

nystagmus 1, congenital, X-linkedSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010693

Submitter: PanelApp Australia

nystagmus 1, congenital, X-linkedDEFINITIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010693

Submitter: G2P

Clinical Genomic Database (CGD)

Nystagmus 1, congenital, X-linkedXL

Manifestation: Neurologic

Intervention: General

Rationale: 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

Refs: 16020310; 16240070; 17013395; 18087240; 17768376; 19072571; 17962394; 21746984; 21303855; 21386928; 21746984; 22065930; 22262942; 22490987Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FRMD7 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 433
Inborn genetic diseasesTotal: 81
not specifiedTotal: 72
Nystagmus 1, congenital, X-linkedTotal: 58
FRMD7-related disordersTotal: 20
FRMD7-related disorderTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_194277.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
10
clinvar
70
clinvar
4
clinvar
 85
missense
9
clinvar
14
clinvar
261
clinvar
44
clinvar
3
clinvar
 331
nonsense
11
clinvar
6
clinvar
1
clinvar
 18
start loss
3
clinvar
 3
frameshift
11
clinvar
11
clinvar
1
clinvar
 23
splice donor/acceptor (+/-2bp)
5
clinvar
7
clinvar
5
clinvar
 17
Total40382771157477

Highest pathogenic variant AF is 0.000114164315

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_194277.3RefSeqNP_919253.112MANE Select
ENST00000298542.9EnsemblENSP00000298542.312MANE Select
NM_001306193.2RefSeqNP_001293122.112Standard
ENST00000370879.5EnsemblENSP00000359916.18Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

  • molecular_function

Cellular Component

  • extracellular space
  • cytoskeleton
  • growth cone
  • neuron projection
  • neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000298542
Coding exons
12
Length
51028
Individuals with no LoFs
125613
Homozygous LoFs
2
Heterozygous LoFs
5
Defined
125620
p
0.0000279
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.7042252570.8760.00001844753
Missense (PolyPhen)79109.960.718422091
Synonymous0.2589093.20.9660.000006631321
Loss of Function3.54421.80.1830.00000163402

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000730.000058rare
Ashkenazi Jewish00.0absent
East Asian0.0000720.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000370.000026rare
South Asian00.0absent
Other0.000220.00016rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.181

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
Feedback | API | MCP | Annotate VCF | Sitemap | About | Privacy & Terms
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.