SPOCD1

protein-coding

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

Gene summary

This gene encodes a protein that belongs to the TFIIS family of transcription factors. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

MANE transcript

NM_144569.7

Inheritance

—

ClinVar variants

P:3U:158B:29

Top phenotype

Male infertility with azoospermia or oligozoospermia due to single gene mutation

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr1:31,790,422-31,816,022

External References & Databases

Ensembl (ENSG00000134668)

Transcript & Mutation Effects

hg38 • Region Span ~25.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPOCD1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 176

not providedTotal: 4

Male infertility with azoospermia or oligozoospermia due to single gene mutationTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144569.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	2 clinvar	4
missense		1 clinvar	156 clinvar	26 clinvar		183
nonsense			1 clinvar			1
start loss						0
frameshift		2 clinvar				2
splice donor/acceptor (+/-2bp)						0
Total	0	3	158	27	2	190

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144569.7	RefSeq	NP_653170.3	15	MANE Select
ENST00000360482.7	Ensembl	ENSP00000353670.2	15	MANE Select
NM_001281987.3	RefSeq	NP_001268916.1	15	Standard
NM_001281988.3	RefSeq	NP_001268917.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transcription, DNA-templated
negative regulation of phosphatase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360482
Coding exons: 15
Length: 25630
Individuals with no LoFs: 125644
Homozygous LoFs: 0
Heterozygous LoFs: 104
Defined: 125748
p: 0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.02	590	664	0.889	0.0000363	7736
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00039	0.00038	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00063	0.00062	rare
South Asian	0.00026	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.888
RVIS EVS: 1.45
RVIS percentile EVS: 95.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0730

Gene Damage Prediction

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