RAB40AL

RAB40A like

Basic information

Region (hg38): X:102937272-102938300

Links

ENSG00000102128 ∙ NCBI:282808 ∙ OMIM:300405 ∙ HGNC:25410 ∙ Uniprot:P0C0E4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• X-linked syndromic intellectual disability (Refuted Evidence), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAB40AL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB40AL 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	6	7
missense			10	1	2	13
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	8

Variants in RAB40AL

This is a list of pathogenic ClinVar variants found in the RAB40AL 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-102937320-T-A			Uncertain significance (Dec 18, 2017)
X-102937329-C-A		not specified	Uncertain significance (Jan 10, 2023)
X-102937329-C-T		not specified	Uncertain significance (Mar 29, 2022)
X-102937333-C-T			Benign (Apr 06, 2018)
X-102937376-G-A		not specified	Uncertain significance (Apr 07, 2023)
X-102937387-G-C			Benign (Sep 13, 2022)
X-102937400-A-G			Benign (Sep 13, 2022)
X-102937433-G-T		not specified	Uncertain significance (Jun 02, 2024)
X-102937444-G-A			Benign (Feb 25, 2018)
X-102937494-A-G		Deafness-intellectual disability, Martin-Probst type syndrome	Uncertain significance (-)
X-102937553-A-G		Deafness-intellectual disability, Martin-Probst type syndrome	Uncertain significance (Apr 22, 2020)
X-102937575-G-A		not specified	Likely benign (Nov 11, 2016)
X-102937597-C-T			Benign (Jun 16, 2018)
X-102937663-T-A		not specified	Uncertain significance (May 18, 2022)
X-102937697-C-T		not specified	Uncertain significance (Nov 10, 2022)
X-102937753-C-T			Benign (Sep 13, 2022)
X-102937765-C-T			Benign (Sep 13, 2022)
X-102937803-A-G		not specified	Uncertain significance (Feb 14, 2023)
X-102937822-G-A			Likely benign (Jul 01, 2022)
X-102937823-G-C		not specified	Uncertain significance (Nov 14, 2023)
X-102937848-G-A		not specified	Uncertain significance (Jun 11, 2024)
X-102937911-G-T		not specified	Uncertain significance (Dec 17, 2023)
X-102937957-G-A			Benign (Feb 25, 2018)
X-102937967-G-A		not specified	Uncertain significance (Mar 02, 2023)
X-102937978-C-G		not specified	Conflicting classifications of pathogenicity (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB40AL	protein_coding	protein_coding	ENST00000218249	1	1029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.313	0.500	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.233	136	129	1.06	0.0000113	1812
Missense in Polyphen		63	66.468	0.94783		897
Synonymous	0.474	50	54.5	0.918	0.00000483	574
Loss of Function	0.509	0	0.302	0.00	1.93e-8	4

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000250}.
• Disease: DISEASE: Mental retardation, X-linked, syndromic, Martin-Probst type (MRXSMP) [MIM:300519]: A rare neurodevelopmental disorder characterized by mental retardation, sensorineural hearing loss, short stature and craniofacial dysmorphisms. Patients also exhibit abnormal teeth, widely spaced nipples, abnormal dermatoglyphics, renal insufficiency, and impaired haematopoiesis. Mental retardation is defined as significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:22581972}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.468
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.206

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.232

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;protein ubiquitination;Rab protein signal transduction
• Cellular component: Golgi membrane;cytoplasm;mitochondrion
• Molecular function: GTPase activity;GTP binding