NEXMIF

neurite extension and migration factor

Basic information

Region (hg38): X:74732856-74925472

Previous symbols: [ "KIAA2022" ]

Links

ENSG00000050030

∙ NCBI:340533 ∙ OMIM:300524 ∙ HGNC:29433 ∙ Uniprot:Q5QGS0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

myoclonic-astatic epilepsy (Supportive), mode of inheritance: Unknown
X-linked intellectual disability, Cantagrel type (Supportive), mode of inheritance: XL
X-linked intellectual disability, Cantagrel type (Strong), mode of inheritance: XL
X-linked complex neurodevelopmental disorder (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 98	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	Craniofacial; Neurologic	15466006; 23615299

ClinVar

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

not_provided (1005 variants)
not_specified (236 variants)
X-linked_intellectual_disability,_Cantagrel_type (133 variants)
NEXMIF-related_disorder (27 variants)
Inborn_genetic_diseases (11 variants)
Intellectual_disability (8 variants)
Seizure (3 variants)
See_cases (2 variants)
Continuous_spike_and_waves_during_slow_sleep (1 variants)
Neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEXMIF gene is commonly pathogenic or not. These statistics are base on transcript: NM_001008537.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	209 clinvar	17 clinvar	230
missense	3 clinvar	1 clinvar	539 clinvar	121 clinvar	33 clinvar	697
nonsense	73 clinvar	10 clinvar		1 clinvar		84
start loss						0
frameshift	116 clinvar	14 clinvar	2 clinvar	1 clinvar		133
splice donor/acceptor (+/-2bp)		1 clinvar	2 clinvar			3
Total	192	26	547	332	50

Highest pathogenic variant AF is 0.0000033056895

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEXMIF	protein_coding	protein_coding	ENST00000055682	3	192599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000321	125687	2	5	125694	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	464	548	0.847	0.0000391	10137
Missense in Polyphen		101	185.61	0.54416		3521
Synonymous	-0.387	214	207	1.03	0.0000147	2866
Loss of Function	4.90	2	31.9	0.0627	0.00000251	619

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000146	0.000146
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000122	0.00000880
Middle Eastern	0.0000722	0.0000544
South Asian	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in neurite outgrowth by regulating cell-cell adhesion via the N-cadherin signaling pathway. May act by regulating expression of protein-coding genes, such as N-cadherins and integrin beta-1 (ITGB1). {ECO:0000250|UniProtKB:D3ZGX1}.;

Recessive Scores

pRec: 0.0964

Intolerance Scores

loftool
rvis_EVS: -0.77
rvis_percentile_EVS: 13.1

Haploinsufficiency Scores

pHI: 0.503
hipred: Y
hipred_score: 0.644
ghis: 0.557

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name: Nexmif
Phenotype

Gene ontology

Biological process: negative regulation of cell-matrix adhesion;negative regulation of cell adhesion mediated by integrin;negative regulation of cell-cell adhesion mediated by cadherin;negative regulation of neuron migration
Cellular component: nucleus;cytoplasm
Molecular function