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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nystagmus 1, congenital, X-linked	XL	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	Neurologic	16020310; 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 (22 variants)
• Nystagmus 1, congenital, X-linked (5 variants)
• Inborn genetic diseases (1 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.

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			2	45	14	61
missense	5	3	170	10	17	205
nonsense	8		1			9
start loss	3				1	4
frameshift	5				1	6
inframe indel		1	5			6
splice donor/acceptor (+/-2bp)	4	4				8
splice region		1	8	3	2	14
non coding			12	18	19	49
Total	25	8	190	73	52

Highest pathogenic variant AF is 0.00000888

Variants in FRMD7

This is a list of pathogenic ClinVar variants found in the FRMD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-132077045-A-T		Nystagmus 1, congenital, X-linked	Likely benign (Jan 13, 2018)
X-132077056-C-T		Nystagmus 1, congenital, X-linked	Benign (Jan 12, 2018)
X-132077116-TAAAC-T		Infantile Nystagmus	Uncertain significance (Jun 14, 2016)
X-132077142-T-C		Nystagmus 1, congenital, X-linked	Likely benign (Jan 13, 2018)
X-132077187-A-G		Nystagmus 1, congenital, X-linked	Likely benign (Jan 13, 2018)
X-132077207-T-A		Nystagmus 1, congenital, X-linked	Benign (Jan 13, 2018)
X-132077272-G-C		Nystagmus 1, congenital, X-linked	Uncertain significance (Jan 13, 2018)
X-132077299-C-A		Nystagmus 1, congenital, X-linked	Uncertain significance (Jan 12, 2018)
X-132077438-G-A		Nystagmus 1, congenital, X-linked	Benign (Jan 12, 2018)
X-132077572-A-G		Nystagmus 1, congenital, X-linked	Uncertain significance (Jan 13, 2018)
X-132077579-C-G		Nystagmus 1, congenital, X-linked	Uncertain significance (Jan 13, 2018)
X-132077587-G-A		Nystagmus 1, congenital, X-linked	Uncertain significance (Jan 13, 2018)
X-132077676-C-G		Nystagmus 1, congenital, X-linked	Uncertain significance (Jan 12, 2018)
X-132077872-T-A			Uncertain significance (Apr 10, 2023)
X-132077878-TA-T			Benign (Dec 18, 2023)
X-132077892-A-G			Uncertain significance (Jul 14, 2023)
X-132077901-G-A			Likely benign (Nov 24, 2022)
X-132077903-G-A			Uncertain significance (Sep 01, 2022)
X-132077905-A-G			Likely benign (Jul 26, 2022)
X-132077907-T-C			Uncertain significance (Jul 10, 2020)
X-132077924-G-A			Uncertain significance (Dec 30, 2022)
X-132077930-T-C			Uncertain significance (Aug 17, 2022)
X-132077946-C-T			Uncertain significance (Aug 19, 2023)
X-132077947-ATCT-A			Uncertain significance (Mar 17, 2023)
X-132077949-C-A			Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRMD7	protein_coding	protein_coding	ENST00000298542	12	51028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.730	0.270	125613	2	5	125620	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.704	225	257	0.876	0.0000184	4753
Missense in Polyphen		79	109.96	0.71842		2091
Synonymous	0.258	90	93.2	0.966	0.00000663	1321
Loss of Function	3.54	4	21.8	0.183	0.00000163	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000729	0.0000729
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000723	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000368	0.0000264
Middle Eastern	0.0000723	0.0000544
South Asian	0.00	0.00
Other	0.000222	0.000163

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

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

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

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