PRAF2

PRA1 domain family member 2, the group of YIP family

Basic information

Region (hg38): X:49071161-49074002

Links

ENSG00000243279 ∙ NCBI:11230 ∙ OMIM:300840 ∙ HGNC:28911 ∙ Uniprot:O60831 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRAF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAF2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in PRAF2

This is a list of pathogenic ClinVar variants found in the PRAF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-49071963-T-C		not specified	Uncertain significance (Mar 19, 2024)
X-49071990-G-A		not specified	Uncertain significance (Jun 07, 2023)
X-49072000-C-A		not specified	Uncertain significance (Nov 09, 2023)
X-49072444-C-T		not specified	Uncertain significance (Oct 20, 2021)
X-49072454-T-C		not specified	Uncertain significance (Mar 16, 2022)
X-49072465-G-C		not specified	Uncertain significance (Dec 31, 2023)
X-49072517-C-T		not specified	Uncertain significance (Aug 08, 2023)
X-49072646-C-T		not specified	Uncertain significance (Aug 21, 2024)
X-49073837-A-G		not specified	Uncertain significance (Nov 07, 2022)
X-49073851-G-C		not specified	Uncertain significance (Jan 04, 2022)
X-49073882-G-C		not specified	Uncertain significance (Feb 07, 2023)
X-49073893-C-A		not specified	Uncertain significance (Dec 18, 2023)
X-49073929-G-C		not specified	Uncertain significance (Dec 01, 2022)
X-49073983-G-A		not specified	Uncertain significance (Aug 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAF2	protein_coding	protein_coding	ENST00000376390	3	2918

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.742	0.248	123929	0	1	123930	0.00000403

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	52	81.9	0.635	0.00000702	1096
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000125	0.00000901
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.242
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.206

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Praf2
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: protein transport;L-glutamate transmembrane transport
• Cellular component: endosome membrane;integral component of membrane