NALF2

NALCN channel auxiliary factor 2

Basic information

Region (hg38): X:69504326-69532508

Previous symbols: [ "TMEM28", "CXorf63", "FAM155B" ]

Links

ENSG00000130054 ∙ NCBI:27112 ∙ ∙ HGNC:30701 ∙ Uniprot:O75949 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NALF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NALF2 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		2
missense			38	2		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	4	0

Variants in NALF2

This is a list of pathogenic ClinVar variants found in the NALF2 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-69505310-G-A		not specified	Uncertain significance (Dec 10, 2024)
X-69505315-A-T		not specified	Uncertain significance (Apr 25, 2022)
X-69505344-G-A		not specified	Uncertain significance (Feb 11, 2025)
X-69505350-G-A		not specified	Uncertain significance (Oct 29, 2021)
X-69505357-G-C		not specified	Uncertain significance (Oct 12, 2024)
X-69505380-C-G		not specified	Uncertain significance (May 24, 2024)
X-69505385-G-T		not specified	Uncertain significance (Jun 25, 2024)
X-69505401-C-T		not specified	Uncertain significance (Aug 19, 2024)
X-69505470-T-C		not specified	Uncertain significance (Jun 05, 2023)
X-69505490-C-T		not specified	Uncertain significance (Aug 26, 2024)
X-69505494-C-G		not specified	Uncertain significance (Apr 07, 2023)
X-69505506-G-A		not specified	Uncertain significance (Feb 16, 2023)
X-69505520-C-T		not specified	Uncertain significance (Jan 28, 2025)
X-69505526-T-C		not specified	Uncertain significance (Dec 03, 2024)
X-69505598-G-C		not specified	Uncertain significance (Jan 03, 2024)
X-69505625-G-T		not specified	Uncertain significance (Dec 15, 2023)
X-69505737-C-A		not specified	Uncertain significance (Jan 23, 2025)
X-69505753-C-T			Likely benign (Jan 01, 2023)
X-69505769-G-A		not specified	Uncertain significance (Aug 12, 2021)
X-69505773-C-T		not specified	Uncertain significance (May 25, 2022)
X-69505775-C-G		not specified	Uncertain significance (Mar 05, 2025)
X-69505797-T-A		not specified	Uncertain significance (Mar 18, 2024)
X-69505805-G-T		not specified	Uncertain significance (Dec 22, 2023)
X-69505857-G-A		not specified	Uncertain significance (Oct 25, 2024)
X-69505880-G-A		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NALF2	protein_coding	protein_coding	ENST00000252338	3	27268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.813	0.186	125620	5	6	125631	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.379	184	170	1.08	0.0000129	3013
Missense in Polyphen		93	89.856	1.035		1589
Synonymous	-1.44	93	76.9	1.21	0.00000584	994
Loss of Function	2.62	1	9.90	0.101	6.38e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000113	0.0000981
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.0000792
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.0994
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.255
• hipred: Y
• hipred_score: 0.737

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem28

Gene ontology

• Biological process: calcium ion import across plasma membrane
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: stretch-activated, cation-selective, calcium channel activity