SNX12

protein-coding

sorting nexin 12, the group of Sorting nexins

Gene summary

This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like some family members. A similar protein in mouse may be involved in regulating the neurite outgrowth. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]

MANE transcript

NM_013346.4

Inheritance

—

ClinVar variants

U:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:71,056,332-71,073,426

External References & Databases

Ensembl (ENSG00000147164)

Transcript & Mutation Effects

hg38 • Region Span ~17.1 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 SNX12 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013346.4. 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			2 clinvar			2
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	21	0	0	21

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013346.4	RefSeq	NP_037478.2	4	MANE Select
ENST00000374274.8	Ensembl	ENSP00000363392.3	4	MANE Select
NM_001256185.2	RefSeq	NP_001243114.1	4	Standard
NM_001256186.2	RefSeq	NP_001243115.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)

Biological Process

negative regulation of gene expression
negative regulation of protein processing
protein transport
regulation of endocytosis
negative regulation of protein catabolic process

Molecular Function

protein binding
enzyme binding
phosphatidylinositol binding

Cellular Component

early endosome
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374274
Coding exons: 4
Length: 9180
Individuals with no LoFs: 124351
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 124352
p: 0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.16	18	68.2	0.264	0.00000559	1057
Missense (PolyPhen)		8	33.284	0.24036		514
Synonymous	0.605	22	25.9	0.849	0.00000194	315
Loss of Function	2.09	0	5.08	0.00	3.88e-7	83

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000012	0.0000089	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in several stages of intracellular trafficking. {ECO:0000250}.;

Recessive Scores

pRec: 0.114

Intolerance Scores

RVIS EVS: 0.04
RVIS percentile EVS: 56.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.575

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low