ACTL9

actin like 9, the group of Actin related proteins

Basic information

Region (hg38): 19:8697400-8698795

Links

ENSG00000181786 ∙ NCBI:284382 ∙ OMIM:619251 ∙ HGNC:28494 ∙ Uniprot:Q8TC94 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR
• spermatogenic failure 53 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 53	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	33626338

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACTL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACTL9 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						0
missense			30	3		33
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	0

Variants in ACTL9

This is a list of pathogenic ClinVar variants found in the ACTL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-8697479-GGACCCTGTTCCTCGTACTGC-G		Spermatogenic failure 53	Uncertain significance (Apr 04, 2024)
19-8697493-G-C		Spermatogenic failure 53	Pathogenic (Apr 01, 2021)
19-8697503-C-T		ACTL9-related disorder	Likely benign (May 12, 2022)
19-8697509-A-G		not specified	Uncertain significance (May 17, 2023)
19-8697531-G-T		not specified	Uncertain significance (Dec 28, 2023)
19-8697564-C-A		Spermatogenic failure 53	Pathogenic (Apr 01, 2021)
19-8697668-G-A		Spermatogenic failure 53	Pathogenic (Apr 01, 2021)
19-8697691-G-C		not specified	Uncertain significance (Dec 07, 2023)
19-8697701-A-G		not specified	Uncertain significance (Feb 28, 2024)
19-8697747-C-A		not specified	Uncertain significance (Apr 07, 2023)
19-8697827-T-C		not specified	Uncertain significance (May 04, 2023)
19-8697846-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-8697860-T-C		not specified	Uncertain significance (Jun 01, 2023)
19-8697879-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-8697914-G-C		not specified	Uncertain significance (Feb 12, 2024)
19-8697921-C-T		not specified	Uncertain significance (Nov 15, 2021)
19-8697948-C-T		not specified	Uncertain significance (Oct 26, 2021)
19-8698020-G-C		not specified	Uncertain significance (Feb 14, 2023)
19-8698080-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-8698092-A-T		not specified	Uncertain significance (Nov 09, 2022)
19-8698101-C-T		not specified	Uncertain significance (Feb 13, 2023)
19-8698102-G-C		not specified	Uncertain significance (Mar 25, 2024)
19-8698126-G-C		not specified	Uncertain significance (Jan 23, 2024)
19-8698137-C-T		not specified	Uncertain significance (Aug 17, 2021)
19-8698182-C-T		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACTL9	protein_coding	protein_coding	ENST00000324436	1	1422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00405	0.870	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.131	279	285	0.978	0.0000196	2623
Missense in Polyphen		104	122.32	0.85023		1127
Synonymous	0.814	133	145	0.914	0.0000112	958
Loss of Function	1.29	5	9.24	0.541	4.00e-7	97

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

Intolerance Scores

• loftool: 0.135
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.272
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Actl9

Gene ontology

• Cellular component: cytoplasm;cytoskeleton