SNX29

protein-coding

sorting nexin 29, the group of Sorting nexins

Gene summary

Predicted to enable phosphatidylinositol binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

RUNDC2A

MANE transcript

NM_032167.5

Inheritance

—

ClinVar variants

U:100B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr16:11,976,734-12,574,287

External References & Databases

Ensembl (ENSG00000048471)

Transcript & Mutation Effects

hg38 • Region Span ~597.6 kb

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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 SNX29 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032167.5. 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			6 clinvar	3 clinvar		9
missense			85 clinvar	3 clinvar		88
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	100	6	0	106

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032167.5	RefSeq	NP_115543.3	21	MANE Select
ENST00000566228.6	Ensembl	ENSP00000456480.1	21	MANE Select
NM_001376490.1	RefSeq	NP_001363419.1	14	Standard
ENST00000562510.1	Ensembl	ENSP00000455327.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

phosphatidylinositol binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000566228
Coding exons: 21
Length: 597553
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 66
Defined: 125748
p: 0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.79	609	497	1.23	0.0000323	5322
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00032	0.00027	rare
South Asian	0.00014	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.56
RVIS percentile EVS: 19.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.147

Gene Damage Prediction

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