NALF1

protein-coding

NALCN channel auxiliary factor 1, the group of MicroRNA protein coding host genes

Gene summary

Predicted to contribute to stretch-activated, monoatomic cation-selective, calcium channel activity. Involved in regulation of neuronal action potential and sodium ion transmembrane transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM155A

MANE transcript

NM_001080396.3

Inheritance

—

ClinVar variants

U:56B:3

Top phenotype

BRCA2-related cancer predisposition

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr13:107,163,510-107,867,496

External References & Databases

Ensembl (ENSG00000204442)

Transcript & Mutation Effects

hg38 • Region Span ~704.0 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 NALF1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 3

BRCA2-related cancer predispositionTotal: 2

Familial pancreatic carcinomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080396.3. 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				1 clinvar		1
missense			53 clinvar	2 clinvar		55
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	56	3	0	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080396.3	RefSeq	NP_001073865.1	3	MANE Select
ENST00000375915.4	Ensembl	ENSP00000365080.1	3	MANE Select

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: ENST00000375915
Coding exons: 3
Length: 698201
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.307	233	247	0.945	0.0000116	2963
Missense (PolyPhen)		110	135.22	0.81352		1607
Synonymous	-0.170	113	111	1.02	0.00000590	889
Loss of Function	3.76	2	20.3	0.0987	8.75e-7	216

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000055	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.214
RVIS EVS: -0.01
RVIS percentile EVS: 53.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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