ACTRT3

protein-coding

actin related protein T3, the group of Actin related proteins

Gene summary

Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and male germ cell nucleus. Predicted to be active in actin cytoskeleton. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032487.5

Inheritance

—

ClinVar variants

U:65B:1

Top phenotype

Dyskeratosis congenita, autosomal dominant 1

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr3:169,766,921-169,769,561

External References & Databases

Ensembl (ENSG00000184378)

Transcript & Mutation Effects

hg38 • Region Span ~2.6 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 ACTRT3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 1

Dyskeratosis congenita, autosomal dominant 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032487.5. 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						0
missense			64 clinvar	1 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	65	1	0	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032487.5	RefSeq	NP_115876.3	2	MANE Select
ENST00000330368.3	Ensembl	ENSP00000333037.1	2	MANE Select
ENST00000956146.1	Ensembl	ENSP00000626205.1	2	Standard
ENST00000956146.2	Ensembl	ENSP00000626205.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

male germ cell nucleus
cytoplasm
cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000330368
Coding exons: 2
Length: 2975
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125747
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.224	201	210	0.956	0.0000103	2459
Missense (PolyPhen)		93	98.261	0.94646		1124
Synonymous	1.36	67	82.8	0.810	0.00000426	737
Loss of Function	-0.202	11	10.3	1.07	4.38e-7	128

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.00033	0.00033	rare
Other	0.00020	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.95
RVIS percentile EVS: 90.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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