PPP1R21

protein phosphatase 1 regulatory subunit 21, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 2:48440598-48515391

Previous symbols: [ "CCDC128", "KLRAQ1" ]

Links

ENSG00000162869 ∙ NCBI:129285 ∙ OMIM:618159 ∙ HGNC:30595 ∙ Uniprot:Q6ZMI0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities (Strong), mode of inheritance: AR
• neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities (Strong), mode of inheritance: AR
• neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities	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	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	29808498; 32985083; 36692708; 34997808; 38356149

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPP1R21 gene.

• Inborn_genetic_diseases (129 variants)
• not_provided (33 variants)
• Neurodevelopmental_disorder_with_hypotonia,_facial_dysmorphism,_and_brain_abnormalities (22 variants)
• PPP1R21-related_disorder (17 variants)
• not_specified (3 variants)
• Neurodevelopmental_disorder_with_hypotonia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R21 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001135629.3. 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				17	1	18
missense	2		135	9		146
nonsense	6	2	2			10
start loss						0
frameshift	6	2				8
splice donor/acceptor (+/-2bp)		3				3
Total	14	7	137	26	1

Highest pathogenic variant AF is 0.000012556426

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R21	protein_coding	protein_coding	ENST00000294952	22	74789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.30e-10	1.00	125699	0	48	125747	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.92	506	398	1.27	0.0000200	5109
Missense in Polyphen		182	166.69	1.0918		2199
Synonymous	-0.991	163	148	1.10	0.00000759	1441
Loss of Function	3.37	25	50.9	0.491	0.00000277	604

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000539	0.000539
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000189	0.000185
European (Non-Finnish)	0.000233	0.000229
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -1.01
• rvis_percentile_EVS: 8.16

Haploinsufficiency Scores

• pHI: 0.210
• hipred: N
• hipred_score: 0.379
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r21

Gene ontology

• Cellular component: membrane