CUTA

protein-coding

cutA divalent cation tolerance homolog

Gene summary

Enables enzyme binding activity. Involved in intracellular protein localization. Located in membrane and mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C6orf82
ACHAP

MANE transcript

NM_001014840.2

Inheritance

—

ClinVar variants

U:29B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr6:33,416,442-33,418,317

External References & Databases

Ensembl (ENSG00000112514)

Transcript & Mutation Effects

hg38 • Region Span ~1.9 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 CUTA variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 24

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001014840.2. 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			25 clinvar			25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	29	1	0	30

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001014840.2	RefSeq	NP_001014840.1	6	MANE Select
ENST00000488034.6	Ensembl	ENSP00000417544.1	6	MANE Select
NM_001014433.3	RefSeq	NP_001014433.2	5	Standard
NM_001014837.2	RefSeq	NP_001014837.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein localization
response to metal ion

Molecular Function

copper ion binding
protein binding
enzyme binding

Cellular Component

membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374500
Coding exons: 6
Length: 1876
Individuals with no LoFs: 125514
Homozygous LoFs: 1
Heterozygous LoFs: 232
Defined: 125747
p: 0.000927

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0521	112	114	0.986	0.00000531	1243
Missense (PolyPhen)		35	38.637	0.90586		421
Synonymous	1.02	41	50.2	0.817	0.00000252	444
Loss of Function	0.0166	10	10.1	0.994	4.33e-7	106

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.0017	0.0017	notable
South Asian	0.00020	0.00020	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May form part of a complex of membrane proteins attached to acetylcholinesterase (AChE).;

Recessive Scores

pRec: 0.235

Intolerance Scores

LoFtool: 0.163
RVIS EVS: 1.13
RVIS percentile EVS: 92.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.282

Gene Damage Prediction

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