GDAP1L1

ganglioside induced differentiation associated protein 1 like 1

Basic information

Region (hg38): 20:44247099-44280947

Links

ENSG00000124194 ∙ NCBI:78997 ∙ ∙ HGNC:4213 ∙ Uniprot:Q96MZ0 ∙ 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 GDAP1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDAP1L1 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in GDAP1L1

This is a list of pathogenic ClinVar variants found in the GDAP1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-44247440-G-A		not specified	Uncertain significance (Jan 17, 2023)
20-44247505-C-G		not specified	Uncertain significance (Jun 16, 2024)
20-44257171-G-A		not specified	Uncertain significance (May 02, 2024)
20-44257198-G-T		not specified	Uncertain significance (Feb 28, 2023)
20-44257219-G-A		not specified	Uncertain significance (May 23, 2023)
20-44257244-G-A		not specified	Uncertain significance (Aug 17, 2021)
20-44257282-C-T		not specified	Uncertain significance (Dec 21, 2021)
20-44257294-A-G		not specified	Uncertain significance (Jul 09, 2021)
20-44258460-G-A		not specified	Uncertain significance (Dec 19, 2023)
20-44258478-G-A		not specified	Uncertain significance (Jan 24, 2024)
20-44258481-C-T		not specified	Uncertain significance (Feb 23, 2023)
20-44258497-G-A		not specified	Uncertain significance (May 24, 2023)
20-44258511-G-A		not specified	Uncertain significance (Aug 30, 2022)
20-44258565-A-G		not specified	Uncertain significance (Oct 17, 2024)
20-44258593-C-T		not specified	Uncertain significance (Sep 22, 2023)
20-44258605-G-A		not specified	Uncertain significance (Dec 27, 2022)
20-44263255-C-A		not specified	Uncertain significance (Nov 20, 2024)
20-44263292-T-G		not specified	Uncertain significance (Apr 08, 2024)
20-44263301-T-C		not specified	Uncertain significance (May 17, 2023)
20-44263314-A-C		not specified	Uncertain significance (May 21, 2024)
20-44263314-A-G		not specified	Uncertain significance (Jan 10, 2022)
20-44264556-G-C		not specified	Uncertain significance (Oct 20, 2024)
20-44279032-G-A		not specified	Uncertain significance (Dec 20, 2022)
20-44279061-T-C		not specified	Uncertain significance (Oct 06, 2021)
20-44279080-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDAP1L1	protein_coding	protein_coding	ENST00000342560	6	33127

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.445	0.554	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	149	221	0.675	0.0000133	2377
Missense in Polyphen		56	88.33	0.63399		971
Synonymous	0.551	90	96.9	0.929	0.00000616	714
Loss of Function	2.75	3	14.2	0.211	6.07e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000599	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000599	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.253
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.786
• hipred: Y
• hipred_score: 0.697
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gdap1l1