ACTRT1

actin related protein T1, the group of Actin related proteins

Basic information

Region (hg38): X:128050962-128052403

Links

ENSG00000123165 ∙ NCBI:139741 ∙ OMIM:300487 ∙ HGNC:24027 ∙ Uniprot:Q8TDG2 ∙ 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 ACTRT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACTRT1 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				2		2
missense			29	4	3	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	6	3

Variants in ACTRT1

This is a list of pathogenic ClinVar variants found in the ACTRT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-128051112-C-A		not specified	Uncertain significance (Oct 19, 2024)
X-128051174-A-T		ACTRT1-related disorder	Benign (Mar 30, 2018)
X-128051176-G-A		not specified	Uncertain significance (Sep 26, 2024)
X-128051191-G-T		not specified	Uncertain significance (Mar 02, 2023)
X-128051228-G-A		not specified	Uncertain significance (Jan 20, 2023)
X-128051253-C-A			Likely benign (Feb 01, 2024)
X-128051268-C-A		ACTRT1-related disorder	Benign (Mar 30, 2018)
X-128051269-C-G		not specified	Uncertain significance (Feb 14, 2023)
X-128051332-T-C		ACTRT1-related disorder	Benign (Mar 29, 2018)
X-128051384-G-A			Uncertain significance (Jul 01, 2023)
X-128051386-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-128051476-G-A			Uncertain significance (-)
X-128051486-A-G		not specified	Uncertain significance (Sep 23, 2023)
X-128051503-C-T		not specified	Likely benign (May 29, 2024)
X-128051516-G-T		not specified	Uncertain significance (Dec 20, 2024)
X-128051596-G-A		not specified	Uncertain significance (Jan 01, 2025)
X-128051621-G-C		not specified	Uncertain significance (Nov 17, 2022)
X-128051626-C-A		not specified	Uncertain significance (May 23, 2023)
X-128051627-G-A		not specified	Uncertain significance (Mar 29, 2022)
X-128051659-A-AT		Male infertility with azoospermia or oligozoospermia due to single gene mutation • ACTRT1-related disorder	Conflicting classifications of pathogenicity (Sep 01, 2023)
X-128051785-G-A		not specified	Uncertain significance (Feb 10, 2025)
X-128051800-T-G		not specified	Uncertain significance (May 02, 2024)
X-128051815-C-T		not specified	Likely benign (Dec 30, 2023)
X-128051854-A-T		not specified	Uncertain significance (Apr 09, 2022)
X-128051911-A-G		ACTRT1-related disorder	Uncertain significance (Jul 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACTRT1	protein_coding	protein_coding	ENST00000371124	1	1440

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00374	0.652	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.24	189	147	1.29	0.0000112	2465
Missense in Polyphen		67	52.542	1.2752		903
Synonymous	-0.344	63	59.6	1.06	0.00000470	771
Loss of Function	0.555	4	5.39	0.742	3.80e-7	115

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates the Hedgehog (SHH) signaling. Binds to the promoter of the SHH signaling mediator, GLI1, and inhibits its expression. {ECO:0000269|PubMed:28869610}.

Intolerance Scores

• loftool: 0.312
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.0574
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Actrt1

Gene ontology

• Biological process: regulation of smoothened signaling pathway;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm;cytoskeleton
• Molecular function: chromatin binding