SPOCD1

SPOC domain containing 1, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 1:31790422-31816022

Links

ENSG00000134668 ∙ NCBI:90853 ∙ OMIM:619038 ∙ HGNC:26338 ∙ Uniprot:Q6ZMY3 ∙ 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 SPOCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPOCD1 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		1	81	16		98
nonsense						0
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	3	81	16	2

Variants in SPOCD1

This is a list of pathogenic ClinVar variants found in the SPOCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-31790608-C-A		not specified	Uncertain significance (Jan 30, 2024)
1-31790652-C-T		not specified	Uncertain significance (Dec 11, 2024)
1-31790667-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-31790668-G-A		not specified	Uncertain significance (Jan 20, 2025)
1-31790670-G-A		not specified	Uncertain significance (Jan 01, 2025)
1-31790674-G-A		not specified	Uncertain significance (Feb 07, 2025)
1-31790712-C-T		not specified	Likely benign (Dec 07, 2021)
1-31790748-G-C		not specified	Uncertain significance (Dec 11, 2024)
1-31790749-G-A		not specified	Uncertain significance (Mar 28, 2022)
1-31790794-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-31790803-G-A		not specified	Uncertain significance (Aug 31, 2023)
1-31790803-G-C		not specified	Uncertain significance (Apr 01, 2024)
1-31790832-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-31790871-G-T		not specified	Uncertain significance (May 30, 2024)
1-31790892-T-C		not specified	Uncertain significance (Feb 22, 2025)
1-31790899-G-GT		Male infertility with azoospermia or oligozoospermia due to single gene mutation	Likely pathogenic (Oct 10, 2023)
1-31790901-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-31790902-G-A		not specified	Likely benign (May 09, 2023)
1-31790920-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-31790929-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-31790967-A-C		not specified	Uncertain significance (Mar 03, 2025)
1-31791016-G-A		not specified	Uncertain significance (Jan 08, 2025)
1-31791049-A-C		not specified	Uncertain significance (May 05, 2023)
1-31791063-G-A		not specified	Uncertain significance (Aug 15, 2023)
1-31791066-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPOCD1	protein_coding	protein_coding	ENST00000360482	15	25630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.49e-12	0.992	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	590	664	0.889	0.0000363	7736
Missense in Polyphen		99	128.61	0.76977		1592
Synonymous	0.947	251	271	0.927	0.0000150	2590
Loss of Function	2.60	26	44.8	0.581	0.00000215	522

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000823	0.000821
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000632	0.000615
Middle Eastern	0.000163	0.000163
South Asian	0.000263	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.888
• rvis_EVS: 1.45
• rvis_percentile_EVS: 95.15

Haploinsufficiency Scores

• pHI: 0.0612
• hipred: N
• hipred_score: 0.273

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0730

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spocd1

Gene ontology

• Biological process: transcription, DNA-templated;negative regulation of phosphatase activity