GDAP2

ganglioside induced differentiation associated protein 2, the group of Macro domain containing|BCH domain containing

Basic information

Region (hg38): 1:117863485-117929621

Links

ENSG00000196505 ∙ NCBI:54834 ∙ OMIM:618128 ∙ HGNC:18010 ∙ Uniprot:Q9NXN4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia, autosomal recessive 27 (Limited), mode of inheritance: AR
• spinocerebellar ataxia, autosomal recessive 27 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia, autosomal recessive 27	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	30084953

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GDAP2 gene.

• Spinocerebellar ataxia, autosomal recessive 27 (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDAP2 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				4	2	6
missense			22	2	1	25
nonsense	2	1				3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region				1	1	2
non coding					1	1
Total	2	3	22	6	4

Highest pathogenic variant AF is 0.0000657

Variants in GDAP2

This is a list of pathogenic ClinVar variants found in the GDAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-117870596-T-G			Likely benign (Mar 01, 2023)
1-117870598-T-C		GDAP2-related disorder	Benign (May 24, 2019)
1-117878138-A-T		not specified	Uncertain significance (Mar 01, 2024)
1-117878149-A-AC		Spinocerebellar ataxia, autosomal recessive 27	Pathogenic (Mar 28, 2019)
1-117878162-A-G		GDAP2-related disorder	Benign (Aug 01, 2019)
1-117881820-T-C		GDAP2-related disorder	Likely benign (Jan 01, 2024)
1-117881830-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-117881831-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-117881834-A-C		Spinocerebellar ataxia, autosomal recessive 27	Uncertain significance (Mar 29, 2024)
1-117881851-T-C		not specified	Uncertain significance (Feb 07, 2023)
1-117881872-T-C		not specified	Uncertain significance (Oct 05, 2023)
1-117883536-T-TC		Spinocerebellar ataxia, autosomal recessive 27	Pathogenic (Mar 28, 2019)
1-117883546-C-T		not specified	Uncertain significance (Feb 02, 2022)
1-117883580-C-A		not specified	Uncertain significance (Jun 06, 2023)
1-117883618-A-G		not specified	Uncertain significance (Aug 02, 2021)
1-117883621-A-C		not specified	Uncertain significance (Feb 06, 2023)
1-117886576-C-A		Spinocerebellar ataxia, autosomal recessive 27	Likely pathogenic (Mar 29, 2024)
1-117886636-G-A		GDAP2-related disorder	Likely pathogenic (Mar 16, 2023)
1-117887697-C-A			Likely pathogenic (Jul 05, 2022)
1-117887758-A-G		not specified	Uncertain significance (Dec 18, 2023)
1-117887766-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-117896840-G-A		Spinocerebellar ataxia, autosomal recessive 27	Pathogenic (Sep 24, 2019)
1-117896938-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-117896981-C-T		not specified	Uncertain significance (Jan 10, 2023)
1-117899094-T-C		GDAP2-related disorder	Likely benign (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDAP2	protein_coding	protein_coding	ENST00000369443	13	66147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-9	0.947	125678	0	66	125744	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.928	219	261	0.838	0.0000129	3228
Missense in Polyphen		95	124.76	0.76144		1521
Synonymous	-0.202	97	94.5	1.03	0.00000464	952
Loss of Function	2.01	19	31.1	0.611	0.00000186	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000301
Ashkenazi Jewish	0.00233	0.00228
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000248	0.000246
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.887
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.391
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.212

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gdap2

Gene ontology

• Biological process: response to retinoic acid
• Cellular component: lysosomal membrane
• Molecular function: protein binding