SNX29

Chr 16

sorting nexin 29

Also known as: A-388D4.1, RUNDC2A

NCBI Gene: 92017 ENSG00000048471 UniProt: Q8TEQ0

SNX29 encodes a protein predicted to bind phosphatidylinositol, which is involved in cellular membrane trafficking and signaling pathways. The gene is extremely intolerant to loss-of-function variation (pLI near 1.0), suggesting mutations would likely cause severe developmental disorders, though specific associated phenotypes have not yet been established in the literature. An autosomal recessive or autosomal dominant inheritance pattern would be expected for any future identified SNX29-related disorders.

ResearchSummary from RefSeq

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

ResearchGenerating clinical summary…

DNmechanismLOEUF 0.74

Clinical Summary— SNX29

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

77 VUS of 132 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.74LOEUF

pLI 0.000

Z-score 2.93

OE 0.52 (0.38–0.74)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-1.79Z-score

OE missense 1.23 (1.15–1.31)

609 obs / 496.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.52 (0.38–0.74)

0≤0.351.4

Missense OE?1.23 (1.15–1.31)

0≤0.61.4

Synonymous OE?1.51

0≤1.21.6

LoF obs/exp: 23 / 44.0Missense obs/exp: 609 / 496.6Syn Z: -5.76

This gene — mechanism propensity

0.7034th %ile

GOF

0.6051th %ile

LOF

0.3453th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

132 submitted variants in ClinVar

ClinVar

Classification Summary

VUS77

Likely Benign6

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	1	76	0	77
Likely Benign	0	3	3	6
Benign	0	0	0	0
Total	1	79	3	83

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

17 pathogenic / likely-pathogenic (of 46) ClinVar copy-number / structural variants overlap SNX29 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →