PRAF2

protein-coding

PRA1 domain family member 2, the group of YIP family

Gene summary

Predicted to be involved in L-glutamate transmembrane transport. Predicted to be located in endosome membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_007213.3

Inheritance

—

ClinVar variants

U:25B:1

Top phenotype

Isolated cerebellar hypoplasia/agenesis

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:49,071,161-49,074,002

External References & Databases

Ensembl (ENSG00000243279)

Transcript & Mutation Effects

hg38 • Region Span ~2.8 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 PRAF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 24

Isolated cerebellar hypoplasia/agenesisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007213.3. 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 clinvar		2
missense			23 clinvar			23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	25	1	0	26

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007213.3	RefSeq	NP_009144.1	3	MANE Select
ENST00000553851.3	Ensembl	ENSP00000451962.2	3	MANE Select
ENST00000376386.3	Ensembl	ENSP00000365566.3	2	Standard
ENST00000376386.4	Ensembl	ENSP00000365566.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport
L-glutamate transmembrane transport

Cellular Component

endosome membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376390
Coding exons: 3
Length: 2918
Individuals with no LoFs: 123929
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 123930
p: 0.00000403

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.17	52	81.9	0.635	0.00000702	1096
Missense (PolyPhen)		23	34.036	0.67576		447
Synonymous	1.97	25	41.1	0.609	0.00000356	418
Loss of Function	1.96	0	4.48	0.00	3.39e-7	58

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)	0.000013	0.0000090	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in ER/Golgi transport and vesicular traffic. Plays a proapoptotic role in cerulenin-induced neuroblastoma apoptosis. {ECO:0000269|PubMed:17975142, ECO:0000269|PubMed:18395978}.;

Recessive Scores

pRec: 0.104

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.206

Gene Damage Prediction

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