ACTL7A

actin like 7A, the group of Actin related proteins

Basic information

Region (hg38): 9:108862266-108863756

Links

ENSG00000187003 ∙ NCBI:10881 ∙ OMIM:604303 ∙ HGNC:161 ∙ Uniprot:Q9Y615 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 86	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	32923619; 34727571; 36593593

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACTL7A gene.

• not_specified (72 variants)
• Spermatogenic_failure_86 (6 variants)
• Male_infertility_with_normal_semen_parameters (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACTL7A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006687.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense	3	1	68	3		75
nonsense	2					2
start loss						0
frameshift	1					1
splice donor/acceptor (+/-2bp)						0
Total	6	1	68	4	0

Highest pathogenic variant AF is 0.0000254032

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACTL7A	protein_coding	protein_coding	ENST00000333999	1	1433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.13e-7	0.421	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.180	268	276	0.970	0.0000170	2836
Missense in Polyphen		118	127.08	0.92852		1332
Synonymous	-0.872	139	127	1.10	0.00000897	897
Loss of Function	0.663	11	13.6	0.806	7.50e-7	144

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

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.98

Haploinsufficiency Scores

• pHI: 0.318
• hipred: N
• hipred_score: 0.248
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Actl7a

Gene ontology

• Biological process: cytoskeleton organization
• Cellular component: male germ cell nucleus;nucleus;cytoplasm;Golgi apparatus;cytoskeleton;motile cilium;protein-containing complex
• Molecular function: structural constituent of cytoskeleton;protein binding