UNC79

protein-coding

unc-79 homolog, NALCN channel complex subunit, the group of Armadillo like helical domain containing

Gene summary

The NALCN channel is responsible for Na(+) leak currents. The protein encoded by this gene, along with UNC80, is an accessory subunit of the NALCN channel that contributes to the Ca(2+) sensitivity of the channel. [provided by RefSeq, Sep 2016]

Previous symbols:

KIAA1409

MANE transcript

NM_001395159.1

Inheritance

ClinVar variants

P:18U:341B:44

Top phenotype

complex neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr14:93,333,219-93,707,876

External References & Databases

Ensembl (ENSG00000133958)

Transcript & Mutation Effects

hg38 • Region Span ~374.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UNC79 variants in ClinVar

12 Conditions Cataloged

Inborn genetic diseasesTotal: 258

not providedTotal: 112

UNC79-related disorderTotal: 28

Neurodevelopmental disorderTotal: 4

UNC79-related neurodevelopmental disorderTotal: 2

Prostate cancerTotal: 1

UNC79-associated seizure disorderTotal: 1

Neuropsychiatric disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395159.1. 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		3 clinvar	12 clinvar	3 clinvar	19
missense			315 clinvar	29 clinvar		344
nonsense	4 clinvar	3 clinvar	6 clinvar			13
start loss						0
frameshift	4 clinvar	3 clinvar	7 clinvar			14
splice donor/acceptor (+/-2bp)		3 clinvar	10 clinvar			13
Total	9	9	341	41	3	403

Highest pathogenic variant AF is 6.852056e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395159.1	RefSeq	NP_001382088.1	52	MANE Select
ENST00000695012.1	Ensembl	ENSP00000511643.1	52	MANE Select
NM_001346218.2	RefSeq	NP_001333147.1	51	Standard
NM_020818.5	RefSeq	NP_065869.3	47	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Stimuli-sensing channels
Ion channel transport
Transport of small molecules

Biological Process

ion transmembrane transport
multicellular organism growth
behavioral response to ethanol

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000256339
Coding exons: 47
Length: 374658
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125747
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.16	934	1.37e+3	0.683	0.0000760	16253
Missense (PolyPhen)		409	727.09	0.56252		8881
Synonymous	1.05	510	541	0.943	0.0000344	4712
Loss of Function	9.40	11	124	0.0888	0.00000663	1436

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the NALCN sodium channel complex, a cation channel activated either by neuropeptides substance P or neurotensin that controls neuronal excitability. {ECO:0000250}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

RVIS EVS: -1.11
RVIS percentile EVS: 6.63

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