SNX31

protein-coding

sorting nexin 31, the group of Sorting nexins

Gene summary

Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in endocytic recycling and intracellular protein transport. Predicted to be part of protein-containing complex. Predicted to be active in early endosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_152628.4

Inheritance

—

ClinVar variants

U:75B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr8:100,572,889-100,663,415

External References & Databases

Ensembl (ENSG00000174226)

Transcript & Mutation Effects

hg38 • Region Span ~90.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SNX31 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152628.4. 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				1 clinvar		1
missense			72 clinvar	7 clinvar		79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	75	8	0	83

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152628.4	RefSeq	NP_689841.3	14	MANE Select
ENST00000311812.7	Ensembl	ENSP00000312368.2	14	MANE Select
NM_001363720.1	RefSeq	NP_001350649.1	11	Standard
ENST00000428383.6	Ensembl	ENSP00000405024.2	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
retrograde transport, endosome to plasma membrane

Molecular Function

protein binding
phosphatidylinositol binding

Cellular Component

early endosome
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000311812
Coding exons: 14
Length: 90528
Individuals with no LoFs: 124103
Homozygous LoFs: 46
Heterozygous LoFs: 1599
Defined: 125748
p: 0.00656

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0561	234	236	0.990	0.0000120	2898
Missense (PolyPhen)		63	61.18	1.0297		784
Synonymous	-0.319	94	90.1	1.04	0.00000493	774
Loss of Function	1.15	23	29.7	0.773	0.00000141	336

Population LoF Frequency

Population	CAF	p-value	Status
African	0.069	0.068	notable
Latino/Admixed American	0.0046	0.0046	notable
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.015	0.015	notable
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00077	0.00076	rare
South Asian	0.00096	0.00095	rare
Other	0.0034	0.0034	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in protein trafficking. {ECO:0000250}.;

Recessive Scores

pRec: 0.0614

Intolerance Scores

LoFtool: 0.953
RVIS EVS: 0.53
RVIS percentile EVS: 80.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.160

Gene Damage Prediction

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