SPATA7

spermatogenesis associated 7

Basic information

Region (hg38): 14:88384923-88470350

Previous symbols: [ "LCA3" ]

Links

ENSG00000042317 ∙ NCBI:55812 ∙ OMIM:609868 ∙ HGNC:20423 ∙ Uniprot:Q9P0W8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Supportive), mode of inheritance: AD
• Leber congenital amaurosis (Supportive), mode of inheritance: AD
• severe early-childhood-onset retinal dystrophy (Supportive), mode of inheritance: AR
• Leber congenital amaurosis 3 (Definitive), mode of inheritance: AR
• Leber congenital amaurosis 3 (Definitive), mode of inheritance: AR
• Leber congenital amaurosis 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leber congenital amaurosis 3; Retitinitis pigmentosa, juvenile, SPATA7-related	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	Ophthalmologic	9799089; 18936139; 19268277; 21310915

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPATA7 gene.

• Leber congenital amaurosis 3 (357 variants)
• Retinitis pigmentosa (51 variants)
• not provided (39 variants)
• Inborn genetic diseases (21 variants)
• not specified (16 variants)
• Leber congenital amaurosis (10 variants)
• Retinitis pigmentosa 94, variable age at onset (6 variants)
• SPATA7-Related Disorders (4 variants)
• - (3 variants)
• Retinal dystrophy (3 variants)
• Autosomal recessive retinitis pigmentosa (1 variants)
• Galactosylceramide beta-galactosidase deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA7 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			5	56	3	64
missense			181	8	2	191
nonsense	5	6				11
start loss		1				1
frameshift	16	5	3			24
inframe indel			2			2
splice donor/acceptor (+/-2bp)	3	5	1			9
splice region			9	11	1	21
non coding		1	4	20	8	33
Total	24	18	196	84	13

Highest pathogenic variant AF is 0.0000328

Variants in SPATA7

This is a list of pathogenic ClinVar variants found in the SPATA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-88385707-A-C		Leber congenital amaurosis 3 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
14-88385708-G-A		Retinitis pigmentosa • Leber congenital amaurosis 3	Uncertain significance (Jan 13, 2018)
14-88385724-C-T		Leber congenital amaurosis 3 • Retinitis pigmentosa	Conflicting classifications of pathogenicity (Apr 27, 2017)
14-88385757-G-A		Leber congenital amaurosis 3 • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
14-88385787-G-T		Retinitis pigmentosa • Leber congenital amaurosis 3	Uncertain significance (Jan 13, 2018)
14-88385821-G-A		Leber congenital amaurosis 3 • Leber congenital amaurosis	Conflicting classifications of pathogenicity (Jan 07, 2023)
14-88385821-G-T		Leber congenital amaurosis	Likely pathogenic (Jul 05, 2022)
14-88385822-G-A		not specified • Retinitis pigmentosa • Leber congenital amaurosis 3 • Retinal dystrophy	Benign (Jan 31, 2024)
14-88385822-G-C		Leber congenital amaurosis 3	Uncertain significance (May 22, 2022)
14-88385823-ATGGCAGCCGGAGAGGTAAAGGGCAGC-A			Pathogenic (May 28, 2019)
14-88385828-A-C		Leber congenital amaurosis 3	Uncertain significance (Sep 05, 2020)
14-88385830-C-T		Leber congenital amaurosis 3	Likely benign (Oct 13, 2022)
14-88385831-C-T		Leber congenital amaurosis 3	Uncertain significance (Jun 13, 2022)
14-88385837-G-A		Leber congenital amaurosis	Pathogenic (May 09, 2017)
14-88385837-G-C		Leber congenital amaurosis 3	Uncertain significance (Aug 05, 2021)
14-88385837-G-T		Leber congenital amaurosis 3	Uncertain significance (May 18, 2022)
14-88385838-G-C		Leber congenital amaurosis 3	Pathogenic (-)
14-88385839-T-A		Leber congenital amaurosis 3	Pathogenic (Aug 10, 2023)
14-88385844-G-A		Leber congenital amaurosis 3 • Retinitis pigmentosa	Conflicting classifications of pathogenicity (Oct 13, 2023)
14-88385848-G-A		Leber congenital amaurosis 3	Likely benign (Mar 08, 2023)
14-88385935-TG-T			Benign (May 28, 2019)
14-88391360-AT-A		Leber congenital amaurosis 3	Benign (May 12, 2023)
14-88391362-T-G		Leber congenital amaurosis 3	Benign (Jan 31, 2024)
14-88391363-T-TC		Leber congenital amaurosis 3	Likely benign (Oct 22, 2021)
14-88391369-T-C		Leber congenital amaurosis 3	Likely benign (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA7	protein_coding	protein_coding	ENST00000393545	12	85427

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.18e-13	0.192	125571	1	176	125748	0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0409	311	313	0.993	0.0000160	3930
Missense in Polyphen		84	86.19	0.97459		1126
Synonymous	1.50	98	119	0.825	0.00000631	1101
Loss of Function	0.945	22	27.3	0.805	0.00000142	357

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000718	0.000717
Ashkenazi Jewish	0.00	0.00
East Asian	0.00659	0.00655
Finnish	0.000185	0.000139
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.00659	0.00655
South Asian	0.000164	0.000163
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in photoreceptor cells maintenance (By similarity). It is required for recruitment and proper localization of RPGRIP1 to the photoreceptor connecting cilium (CC), as well as protein trafficking across the CC to the outer segments (By similarity). {ECO:0000250|UniProtKB:Q80VP2}.
• Disease: DISEASE: Leber congenital amaurosis 3 (LCA3) [MIM:604232]: A severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. {ECO:0000269|PubMed:19268277}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa autosomal recessive (ARRP) [MIM:268000]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:19268277}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.987
• rvis_EVS: 1.14
• rvis_percentile_EVS: 92.3

Haploinsufficiency Scores

• pHI: 0.0853
• hipred: N
• hipred_score: 0.146
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata7
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: visual perception;photoreceptor cell maintenance;response to stimulus;protein localization to photoreceptor outer segment;protein localization to photoreceptor connecting cilium
• Cellular component: nucleoplasm;mitochondrion;cytosol;axoneme;microtubule cytoskeleton;photoreceptor connecting cilium;ciliary basal body
• Molecular function: protein binding