SNX29

sorting nexin 29, the group of Sorting nexins

Basic information

Region (hg38): 16:11976733-12574287

Previous symbols: [ "RUNDC2A" ]

Links

ENSG00000048471 ∙ NCBI:92017 ∙ ∙ HGNC:30542 ∙ Uniprot:Q8TEQ0 ∙ 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 SNX29 gene.

• Inborn genetic diseases (26 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX29 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				3		3
missense			26	2		28
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	5	0

Variants in SNX29

This is a list of pathogenic ClinVar variants found in the SNX29 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-12003001-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-12027351-G-A		not specified	Uncertain significance (Jun 30, 2022)
16-12042902-G-A		not specified	Uncertain significance (May 11, 2022)
16-12042917-G-A		not specified	Uncertain significance (Mar 07, 2023)
16-12042950-C-T		not specified	Uncertain significance (Apr 07, 2022)
16-12042965-C-T		not specified	Uncertain significance (Feb 05, 2024)
16-12043008-G-A		not specified	Uncertain significance (Aug 17, 2022)
16-12043016-C-G		not specified	Uncertain significance (Jan 31, 2024)
16-12043022-G-A		not specified	Uncertain significance (Aug 12, 2022)
16-12043041-A-G		not specified	Uncertain significance (May 31, 2022)
16-12043049-A-G		not specified	Uncertain significance (Dec 19, 2023)
16-12043061-G-A		not specified	Uncertain significance (Dec 26, 2023)
16-12043064-C-T		not specified	Uncertain significance (May 16, 2023)
16-12046386-C-T		not specified	Uncertain significance (Mar 29, 2023)
16-12046430-A-G		not specified	Uncertain significance (Oct 12, 2021)
16-12048378-A-G		not specified	Uncertain significance (Nov 21, 2022)
16-12048457-C-G			Likely benign (Mar 01, 2023)
16-12048497-G-C		not specified	Uncertain significance (Nov 03, 2022)
16-12048521-C-G		not specified	Uncertain significance (Mar 01, 2023)
16-12048551-G-A		not specified	Uncertain significance (Jan 17, 2023)
16-12048583-C-T			Likely benign (Mar 01, 2022)
16-12048618-C-T		not specified	Uncertain significance (Jun 03, 2022)
16-12051868-G-T		not specified	Uncertain significance (Aug 09, 2021)
16-12051939-G-A		not specified	Uncertain significance (Jan 26, 2022)
16-12051951-A-T			Likely benign (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX29	protein_coding	protein_coding	ENST00000566228	21	597553

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.62e-10	0.999	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.79	609	497	1.23	0.0000323	5322
Missense in Polyphen		187	167.42	1.1169		1724
Synonymous	-5.76	309	204	1.51	0.0000145	1529
Loss of Function	2.93	23	44.0	0.523	0.00000211	530

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000680	0.000676
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000113	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000316	0.000273
Middle Eastern	0.000113	0.000109
South Asian	0.000138	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.226
• hipred: N
• hipred_score: 0.306
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.147

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx29
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Molecular function: phosphatidylinositol binding