NALF2

protein-coding

NALCN channel auxiliary factor 2

Gene summary

This gene encodes a product belonging to a family of proteins with unknown function. The presence of two transmembrane domains suggests that this protein is a multi-pass membrane protein. [provided by RefSeq, Sep 2011]

Previous symbols:

TMEM28
CXorf63
FAM155B

MANE transcript

NM_015686.3

Inheritance

—

ClinVar variants

U:71B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chrX:69,504,326-69,532,508

External References & Databases

Ensembl (ENSG00000130054)

Transcript & Mutation Effects

hg38 • Region Span ~28.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NALF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015686.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	2 clinvar		6
missense			66 clinvar	2 clinvar		68
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	4	0	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015686.3	RefSeq	NP_056501.2	3	MANE Select
ENST00000252338.5	Ensembl	ENSP00000252338.5	3	MANE Select
ENST00001124247.1	Ensembl	ENSP00000794052.1	2	Standard
ENST00001124248.1	Ensembl	ENSP00000794053.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

calcium ion import across plasma membrane

Molecular Function

stretch-activated, cation-selective, calcium channel activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252338
Coding exons: 3
Length: 27268
Individuals with no LoFs: 125620
Homozygous LoFs: 5
Heterozygous LoFs: 6
Defined: 125631
p: 0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.379	184	170	1.08	0.0000129	3013
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000077	0.000062	rare
Latino/Admixed American	0.000037	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.000079	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.0994
RVIS EVS: 0.46
RVIS percentile EVS: 78.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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