NALF1

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

Basic information

Region (hg38): 13:107163509-107867496

Previous symbols: [ "FAM155A" ]

Links

ENSG00000204442 ∙ NCBI:728215 ∙ OMIM:619899 ∙ HGNC:33877 ∙ Uniprot:B1AL88 ∙ 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 NALF1 gene.

• Inborn genetic diseases (7 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NALF1 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				1		1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	1

Variants in NALF1

This is a list of pathogenic ClinVar variants found in the NALF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-107170569-T-C			Likely benign (Apr 01, 2023)
13-107170588-G-C		not specified	Uncertain significance (Jul 27, 2022)
13-107170646-T-C		not specified	Uncertain significance (Oct 10, 2023)
13-107170681-G-T		not specified	Uncertain significance (Jan 29, 2024)
13-107170696-A-G		not specified	Uncertain significance (Nov 29, 2023)
13-107170696-A-T		not specified	Uncertain significance (Sep 06, 2022)
13-107170717-T-C		not specified	Uncertain significance (Sep 22, 2022)
13-107210680-T-C		not specified	Uncertain significance (Sep 26, 2022)
13-107865729-A-C		not specified	Uncertain significance (Feb 15, 2023)
13-107865959-G-A		not specified	Uncertain significance (Mar 06, 2023)
13-107865998-G-A		not specified	Uncertain significance (Feb 06, 2023)
13-107866001-G-A		not specified	Likely benign (Dec 15, 2023)
13-107866014-A-G		not specified	Uncertain significance (May 05, 2023)
13-107866064-G-A		not specified	Uncertain significance (Jun 21, 2023)
13-107866104-C-G		not specified	Uncertain significance (Apr 22, 2022)
13-107866179-C-T		not specified	Uncertain significance (Sep 17, 2021)
13-107866187-T-G		not specified	Uncertain significance (Nov 08, 2021)
13-107866209-T-G		not specified	Uncertain significance (Dec 14, 2021)
13-107866217-G-A		not specified	Uncertain significance (Jun 05, 2023)
13-107866224-C-T		not specified	Uncertain significance (Mar 16, 2022)
13-107866233-G-A		not specified	Uncertain significance (Jan 26, 2023)
13-107866256-G-C		not specified	Uncertain significance (Sep 26, 2023)
13-107866358-TGCTGCTGCC-T			Benign (Jan 01, 2023)
13-107866459-C-G		not specified	Uncertain significance (Aug 17, 2022)
13-107866461-A-C		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NALF1	protein_coding	protein_coding	ENST00000375915	3	698201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0241	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.307	233	247	0.945	0.0000116	2963
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000550	0.0000352
Middle Eastern	0.000111	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.214
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.226
• hipred: Y
• hipred_score: 0.789
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam155a

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