NEXMIF

neurite extension and migration factor

Basic information

Region (hg38): X:74732855-74925472

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 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 (783 variants)
• Inborn genetic diseases (145 variants)
• X-linked intellectual disability, Cantagrel type (86 variants)
• not specified (29 variants)
• NEXMIF-related condition (7 variants)
• Intellectual disability (6 variants)
• See cases (2 variants)
• Continuous spike and waves during slow sleep (1 variants)
• History of 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.

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			6	161	16	183
missense		1	384	46	40	471
nonsense	56	7	1			64
start loss						0
frameshift	86	8	2	1		97
inframe indel			4	2		6
splice donor/acceptor (+/-2bp)			2			2
splice region			4			4
non coding				11		11
Total	142	16	399	221	56

Variants in NEXMIF

This is a list of pathogenic ClinVar variants found in the NEXMIF 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-74739411-G-A			Likely benign (Jan 13, 2022)
X-74739411-G-C			Uncertain significance (Jul 06, 2022)
X-74739425-T-C			Uncertain significance (May 20, 2022)
X-74739427-C-T		NEXMIF-related disorder	Uncertain significance (Jul 17, 2023)
X-74739447-A-G		not specified • NEXMIF-related disorder	Benign/Likely benign (Mar 01, 2024)
X-74739448-G-A			Uncertain significance (Nov 11, 2023)
X-74739450-T-C			Likely benign (Jun 04, 2022)
X-74739454-A-T			Uncertain significance (Aug 10, 2023)
X-74739462-G-A		NEXMIF-related disorder	Benign/Likely benign (Jun 18, 2023)
X-74739463-G-A			Uncertain significance (Oct 27, 2022)
X-74739463-G-T		not specified	Benign/Likely benign (Oct 29, 2023)
X-74739464-T-C			Benign (Sep 01, 2022)
X-74739478-A-C		NEXMIF-related disorder	Uncertain significance (Feb 22, 2024)
X-74739478-A-G			Uncertain significance (Jun 29, 2022)
X-74739480-G-C		See cases	Uncertain significance (Nov 05, 2018)
X-74739484-T-C			Uncertain significance (Jul 04, 2022)
X-74739489-G-A			Likely benign (Dec 11, 2023)
X-74739491-C-T			Uncertain significance (Mar 08, 2023)
X-74739492-G-A			Benign (Sep 19, 2023)
X-74739492-G-T			Likely benign (Dec 09, 2023)
X-74739496-T-C			Uncertain significance (Apr 08, 2019)
X-74739498-C-T			Uncertain significance (Mar 23, 2021)
X-74739500-T-C			Uncertain significance (Jun 18, 2023)
X-74739511-C-A			Likely benign (Sep 09, 2019)
X-74739511-C-T			Likely benign (Sep 30, 2023)

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

• 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_gene_trap: N

Mouse Genome Informatics

• Gene name: Nexmif

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