SPATC1L

spermatogenesis and centriole associated 1 like

Basic information

Region (hg38): 21:46161148-46184476

Previous symbols: [ "C21orf56" ]

Links

ENSG00000160284 ∙ NCBI:84221 ∙ OMIM:612412 ∙ HGNC:1298 ∙ Uniprot:Q9H0A9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPATC1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATC1L 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				1		1
missense			31	3	4	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	34	4	4

Variants in SPATC1L

This is a list of pathogenic ClinVar variants found in the SPATC1L region.

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

Position	Type	Phenotype	Significance	ClinVar
21-46161387-C-T		not specified	Uncertain significance (Oct 06, 2021)
21-46161474-C-T		not specified	Uncertain significance (Mar 16, 2024)
21-46161480-T-C		not specified	Uncertain significance (Dec 07, 2021)
21-46161491-C-T		not specified	Uncertain significance (Sep 26, 2023)
21-46161509-C-T		not specified	Benign (Apr 19, 2019)
21-46161510-T-C		not specified	Uncertain significance (Apr 07, 2023)
21-46161521-T-A		not specified	Uncertain significance (May 17, 2023)
21-46161539-C-T		not specified	Uncertain significance (Oct 06, 2023)
21-46161556-G-C			Uncertain significance (Feb 17, 2020)
21-46161576-C-T		not specified	Uncertain significance (Sep 17, 2021)
21-46161584-G-A		not specified	Likely benign (Feb 16, 2023)
21-46161594-C-A			Benign (Sep 29, 2017)
21-46161599-C-T		not specified	Uncertain significance (Sep 22, 2023)
21-46161623-C-A		not specified	Uncertain significance (Jul 14, 2021)
21-46161635-G-A		not specified	Uncertain significance (Aug 16, 2022)
21-46161645-G-A		not specified	Uncertain significance (Jan 23, 2024)
21-46161660-G-A		not specified	Uncertain significance (Mar 29, 2023)
21-46161702-A-G		not specified	Uncertain significance (Dec 16, 2023)
21-46161921-C-T		not specified	Benign (Jan 11, 2019)
21-46161923-A-G		not specified	Uncertain significance (Nov 09, 2023)
21-46161955-G-A			Likely benign (Jun 01, 2022)
21-46161957-A-G		not specified	Uncertain significance (Sep 20, 2023)
21-46161983-T-C		not specified	Uncertain significance (Mar 05, 2024)
21-46161996-G-A		not specified	Uncertain significance (Sep 23, 2023)
21-46162020-C-T		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATC1L	protein_coding	protein_coding	ENST00000291672	4	23329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.71e-8	0.0687	125444	0	49	125493	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.291	199	211	0.944	0.0000156	2152
Missense in Polyphen		73	75.206	0.97066		780
Synonymous	-1.84	136	111	1.22	0.00000940	726
Loss of Function	-0.488	11	9.39	1.17	4.80e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000804	0.000782
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000218
Finnish	0.0000977	0.0000924
European (Non-Finnish)	0.0000924	0.0000794
Middle Eastern	0.000223	0.000218
South Asian	0.000367	0.000359
Other	0.000364	0.000327

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 1.2
• rvis_percentile_EVS: 92.92

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.208
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spatc1l
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;centrosome
• Molecular function: molecular_function;protein binding