GPALPP1

GPALPP motifs containing 1

Basic information

Region (hg38): 13:44989529-45037669

Previous symbols: [ "KIAA1704" ]

Links

ENSG00000133114 ∙ NCBI:55425 ∙ ∙ HGNC:20298 ∙ Uniprot:Q8IXQ4 ∙ 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 GPALPP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPALPP1 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	1		4
Total	0	0	29	2	0

Variants in GPALPP1

This is a list of pathogenic ClinVar variants found in the GPALPP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-44989686-C-A		not specified	Uncertain significance (Dec 19, 2023)
13-44989700-G-A		not specified	Uncertain significance (Jul 13, 2021)
13-44989720-C-A		not specified	Uncertain significance (Feb 06, 2023)
13-45004307-G-A		not specified	Uncertain significance (Oct 06, 2022)
13-45004343-A-G		not specified	Uncertain significance (Jul 08, 2022)
13-45004377-G-A		not specified	Uncertain significance (Mar 06, 2025)
13-45004377-G-T		not specified	Uncertain significance (Dec 19, 2023)
13-45006218-C-G		not specified	Uncertain significance (Feb 07, 2023)
13-45006224-G-T		not specified	Uncertain significance (Sep 21, 2023)
13-45006229-C-T			Likely benign (Jul 01, 2022)
13-45006250-T-A		not specified	Uncertain significance (Jul 05, 2024)
13-45008848-G-A		not specified	Uncertain significance (Oct 08, 2024)
13-45008866-A-G		not specified	Uncertain significance (Dec 07, 2024)
13-45014976-G-T		not specified	Uncertain significance (Jul 06, 2021)
13-45014991-A-G		not specified	Uncertain significance (Sep 01, 2021)
13-45015025-C-T		not specified	Uncertain significance (Dec 07, 2024)
13-45015069-A-G		not specified	Uncertain significance (Oct 26, 2022)
13-45015432-G-T		not specified	Uncertain significance (Mar 20, 2024)
13-45015441-A-C		not specified	Uncertain significance (Feb 22, 2023)
13-45015550-G-A		not specified	Uncertain significance (Jul 30, 2024)
13-45020343-C-T		not specified	Uncertain significance (Dec 14, 2024)
13-45020384-T-C		not specified	Uncertain significance (Feb 03, 2022)
13-45020397-A-G		not specified	Uncertain significance (Feb 27, 2025)
13-45020420-T-C		not specified	Uncertain significance (Jul 23, 2024)
13-45027800-G-A		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPALPP1	protein_coding	protein_coding	ENST00000361121	8	44060

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000172	0.887	125698	0	49	125747	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0297	180	179	1.01	0.00000846	2256
Missense in Polyphen		35	38.708	0.90421		497
Synonymous	0.952	53	62.6	0.847	0.00000319	605
Loss of Function	1.51	10	16.6	0.601	7.61e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000856	0.000852
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.000110	0.000109
South Asian	0.000132	0.000131
Other	0.000334	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0625
• hipred: N
• hipred_score: 0.197
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpalpp1