ISYNA1

inositol-3-phosphate synthase 1

Basic information

Region (hg38): 19:18434388-18438167

Links

ENSG00000105655 ∙ NCBI:51477 ∙ OMIM:611670 ∙ HGNC:29821 ∙ Uniprot:Q9NPH2 ∙ 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 ISYNA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISYNA1 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				4	3	7
missense			30		1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1		1
Total	0	0	30	5	4

Variants in ISYNA1

This is a list of pathogenic ClinVar variants found in the ISYNA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18434920-G-T		not specified	Uncertain significance (Jun 07, 2024)
19-18434935-T-C		not specified	Uncertain significance (Mar 28, 2024)
19-18434937-C-T			Likely benign (Feb 01, 2023)
19-18434964-G-A			Benign (Dec 31, 2019)
19-18434968-C-T		not specified	Uncertain significance (Oct 09, 2024)
19-18434984-C-G		not specified	Uncertain significance (Jan 27, 2025)
19-18435002-T-C		not specified	Uncertain significance (Feb 14, 2025)
19-18435084-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-18435297-G-A		not specified	Uncertain significance (Dec 21, 2023)
19-18435308-T-C		not specified	Uncertain significance (Feb 15, 2025)
19-18435315-C-T		not specified	Uncertain significance (Jul 28, 2021)
19-18435394-G-C			Likely benign (Mar 06, 2018)
19-18435553-C-T			Likely benign (May 02, 2018)
19-18435559-G-T			Likely benign (Feb 20, 2018)
19-18435570-G-A		not specified	Uncertain significance (Jun 01, 2023)
19-18435619-T-C		not specified	Uncertain significance (Feb 13, 2025)
19-18435771-C-T		not specified	Uncertain significance (Jan 28, 2025)
19-18435810-T-C		not specified	Uncertain significance (Feb 01, 2025)
19-18435819-C-T		not specified	Uncertain significance (Dec 21, 2024)
19-18435823-G-T		not specified	Uncertain significance (Jun 30, 2022)
19-18435828-T-C		not specified	Uncertain significance (Jun 01, 2023)
19-18435837-C-T		not specified	Uncertain significance (Apr 06, 2022)
19-18435921-T-C		not specified	Uncertain significance (Oct 06, 2021)
19-18436103-C-T		not specified	Uncertain significance (Aug 03, 2021)
19-18436134-G-A			Benign (Apr 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISYNA1	protein_coding	protein_coding	ENST00000338128	10	3914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000249	0.983	125716	0	29	125745	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	288	355	0.811	0.0000231	3549
Missense in Polyphen		86	149.92	0.57363		1513
Synonymous	-1.35	192	170	1.13	0.0000128	1168
Loss of Function	2.14	11	21.8	0.506	0.00000112	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000190	0.000185
European (Non-Finnish)	0.000132	0.000123
Middle Eastern	0.000163	0.000163
South Asian	0.0000991	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Key enzyme in myo-inositol biosynthesis pathway that catalyzes the conversion of glucose 6-phosphate to 1-myo-inositol 1-phosphate in a NAD-dependent manner. Rate-limiting enzyme in the synthesis of all inositol-containing compounds. {ECO:0000269|PubMed:15024000}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Inositol Phosphate Metabolism;Inositol Metabolism;Inositol phosphate metabolism;Metabolism;<i>myo</i>-inositol <i>de novo</i> biosynthesis;Inositol phosphate metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.115
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.515
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Isyna1

Gene ontology

• Biological process: inositol biosynthetic process;phospholipid biosynthetic process;inositol phosphate metabolic process
• Cellular component: cytoplasm;cytosol
• Molecular function: inositol-3-phosphate synthase activity;protein binding