PISD

phosphatidylserine decarboxylase, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 22:31618491-31662221

Links

ENSG00000241878 ∙ NCBI:23761 ∙ OMIM:612770 ∙ HGNC:8999 ∙ Uniprot:Q9UG56 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Liberfarb syndrome (Moderate), mode of inheritance: AR
• Liberfarb syndrome (Limited), mode of inheritance: AR
• Liberfarb syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Liberfarb syndrome	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	Audiologic/Otolaryngologic; Musculoskeletal; Neurologic; Ophthalmologic	30488656; 30858161; 31263216

ClinVar

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

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PISD 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				41	4	45
missense		1	86	3	4	94
nonsense						0
start loss						0
frameshift	2					2
inframe indel			1			1
splice donor/acceptor (+/-2bp)		2				2
splice region			2	3	2	7
non coding				15	2	17
Total	2	3	87	59	10

Highest pathogenic variant AF is 0.0000854

Variants in PISD

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

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

Position	Type	Phenotype	Significance	ClinVar
22-31619617-G-A			Uncertain significance (May 12, 2022)
22-31619619-G-A			Uncertain significance (Jul 06, 2022)
22-31619626-G-A			Likely benign (Aug 30, 2023)
22-31619640-C-T		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
22-31619641-G-A		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
22-31619650-G-C			Uncertain significance (Jul 03, 2022)
22-31619653-C-T			Uncertain significance (Jul 17, 2021)
22-31619667-A-AAAT			Uncertain significance (Jun 27, 2022)
22-31619669-A-G			Likely benign (Jul 28, 2023)
22-31619684-G-A			Likely benign (Nov 03, 2022)
22-31619685-G-A		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
22-31619689-C-T		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
22-31619699-C-T			Likely benign (Nov 09, 2023)
22-31619702-G-A			Likely benign (Apr 09, 2023)
22-31619726-G-A			Likely benign (Jan 15, 2024)
22-31619739-C-T			Uncertain significance (Aug 17, 2022)
22-31619744-A-G			Likely benign (Aug 06, 2022)
22-31619745-C-G		Inborn genetic diseases	Uncertain significance (Feb 26, 2024)
22-31619745-C-T		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
22-31619752-G-C		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
22-31619755-C-G			Likely benign (Jan 31, 2024)
22-31619755-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 06, 2023)
22-31619756-G-A			Benign (Jan 11, 2024)
22-31619759-C-T			Likely benign (Oct 06, 2023)
22-31619769-G-C			Uncertain significance (Jul 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PISD	protein_coding	protein_coding	ENST00000382151	7	43942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.222	0.777	125710	0	37	125747	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.678	221	251	0.880	0.0000170	2423
Missense in Polyphen		64	84.925	0.75361		855
Synonymous	-2.05	137	110	1.25	0.00000748	772
Loss of Function	2.76	4	15.8	0.253	6.73e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.000795	0.000794
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Plays a central role in phospholipid metabolism and in the interorganelle trafficking of phosphatidylserine. {ECO:0000255|HAMAP-Rule:MF_03208}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Phospholipid Biosynthesis;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Metabolism of lipids;Glycine Serine metabolism;Metabolism;Synthesis of PE;Glycerophospholipid metabolism;FOXA1 transcription factor network;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.195

Intolerance Scores

• loftool: 0.122
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.71

Haploinsufficiency Scores

• pHI: 0.905
• hipred: Y
• hipred_score: 0.588
• ghis: 0.531

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.808

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pisd
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: phosphatidylethanolamine biosynthetic process;protein autoprocessing
• Cellular component: nucleus;mitochondrion;integral component of mitochondrial inner membrane
• Molecular function: phosphatidylserine decarboxylase activity