ALG1L1P

ALG1 like 1, pseudogene

Basic information

Region (hg38): 3:125929272-125990537

Previous symbols: [ "ALG1L" ]

Links

ENSG00000189366 ∙ NCBI:200810 ∙ ∙ HGNC:33721 ∙ ∙ ∙ 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 ALG1L1P gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALG1L1P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7			7
Total	0	0	7	0	0

Variants in ALG1L1P

This is a list of pathogenic ClinVar variants found in the ALG1L1P region.

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

Position	Type	Phenotype	Significance	ClinVar
3-125972073-C-T		not specified	Uncertain significance (May 02, 2024)
3-125972089-C-A		not specified	Uncertain significance (Nov 07, 2023)
3-125972124-G-A		not specified	Uncertain significance (Nov 09, 2023)
3-125972128-C-T		not specified	Uncertain significance (Apr 07, 2023)
3-125972143-C-A		not specified	Uncertain significance (Apr 25, 2023)
3-125972160-T-C		not specified	Uncertain significance (Nov 07, 2023)
3-125972169-G-C		not specified	Uncertain significance (Dec 20, 2021)
3-125975592-C-T		not specified	Uncertain significance (Oct 25, 2023)
3-125975598-C-T		not specified	Uncertain significance (Jul 20, 2021)
3-125975608-G-C		not specified	Uncertain significance (Aug 29, 2022)
3-125975610-G-A		not specified	Likely benign (Jan 31, 2024)
3-125982277-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-125982349-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-125983256-T-C		not specified	Uncertain significance (Apr 15, 2024)
3-125983264-G-T		not specified	Uncertain significance (Nov 08, 2022)
3-125983295-A-C		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALG1L1P	protein_coding	protein_coding	ENST00000340333	5	7765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-8	0.0280	125570	0	21	125591	0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.41	172	103	1.67	0.00000528	1211
Missense in Polyphen		46	32.689	1.4072		428
Synonymous	-2.14	60	42.3	1.42	0.00000237	359
Loss of Function	-1.41	10	6.20	1.61	2.62e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000553	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000628	0.0000617
Middle Eastern	0.0000553	0.0000544
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative glycosyltransferase. {ECO:0000250}.

Intolerance Scores

• loftool: 0.642
• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.24

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0645

Gene Damage Prediction

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

Gene ontology

• Biological process: protein glycosylation;mannosylation
• Cellular component: endoplasmic reticulum
• Molecular function: mannosyltransferase activity