RAPH1

Ras association (RalGDS/AF-6) and pleckstrin homology domains 1, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 2:203394344-203535335

Previous symbols: [ "ALS2CR9", "ALS2CR18" ]

Links

ENSG00000173166 ∙ NCBI:65059 ∙ OMIM:609035 ∙ HGNC:14436 ∙ Uniprot:Q70E73 ∙ 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 RAPH1 gene.

• Inborn genetic diseases (42 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAPH1 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				1		1
missense			42			42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	1	0

Variants in RAPH1

This is a list of pathogenic ClinVar variants found in the RAPH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-203395693-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-203395741-A-G		not specified	Uncertain significance (Aug 02, 2022)
2-203402697-T-A		not specified	Uncertain significance (Aug 19, 2023)
2-203402707-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-203411347-T-A		not specified	Uncertain significance (Feb 10, 2022)
2-203427242-A-C		not specified	Uncertain significance (Apr 25, 2022)
2-203427323-G-A		not specified	Uncertain significance (Jun 30, 2022)
2-203439498-C-T		not specified	Uncertain significance (May 02, 2023)
2-203439524-A-T		not specified	Uncertain significance (Jun 28, 2022)
2-203439579-G-A		not specified	Uncertain significance (Dec 19, 2022)
2-203439796-G-A		not specified	Uncertain significance (Aug 23, 2021)
2-203439819-C-T		not specified	Uncertain significance (Jan 20, 2023)
2-203439855-G-C		not specified	Uncertain significance (Jun 12, 2023)
2-203439900-G-C		not specified	Uncertain significance (Dec 13, 2023)
2-203439933-G-C		not specified	Uncertain significance (Sep 21, 2023)
2-203440009-C-T		not specified	Likely benign (Dec 11, 2023)
2-203440042-C-T		not specified	Uncertain significance (Mar 24, 2023)
2-203440120-G-T		not specified	Uncertain significance (Sep 14, 2022)
2-203440132-G-A		not specified	Uncertain significance (Dec 09, 2023)
2-203440174-G-T		not specified	Uncertain significance (Mar 29, 2023)
2-203440203-G-A		not specified	Uncertain significance (Jun 09, 2022)
2-203440219-C-T		not specified	Uncertain significance (May 27, 2022)
2-203440261-G-A		not specified	Uncertain significance (Apr 28, 2022)
2-203440287-C-A		not specified	Uncertain significance (Mar 23, 2022)
2-203440323-G-A		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAPH1	protein_coding	protein_coding	ENST00000319170	13	141066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000148	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	583	685	0.851	0.0000363	8056
Missense in Polyphen		141	211.63	0.66624		2626
Synonymous	-0.939	277	258	1.07	0.0000143	2640
Loss of Function	5.69	5	47.2	0.106	0.00000249	567

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000124
Ashkenazi Jewish	0.000148	0.0000992
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000776	0.0000703
Middle Eastern	0.000112	0.000109
South Asian	0.0000909	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediator of localized membrane signals. Implicated in the regulation of lamellipodial dynamics. Negatively regulates cell adhesion.

Recessive Scores

• pRec: 0.270

Intolerance Scores

• loftool: 0.366
• rvis_EVS: -2.61
• rvis_percentile_EVS: 0.81

Haploinsufficiency Scores

• pHI: 0.260
• hipred: N
• hipred_score: 0.364
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.606

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Raph1
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; neoplasm; pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; digestive/alimentary phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: signal transduction;axon extension
• Cellular component: cytosol;cytoskeleton;plasma membrane;nuclear body;lamellipodium;filopodium
• Molecular function: protein binding