AHCYL2

adenosylhomocysteinase like 2

Basic information

Region (hg38): 7:129225029-129430211

Links

ENSG00000158467 ∙ NCBI:23382 ∙ OMIM:616520 ∙ HGNC:22204 ∙ Uniprot:Q96HN2 ∙ 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 AHCYL2 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AHCYL2 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in AHCYL2

This is a list of pathogenic ClinVar variants found in the AHCYL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-129225099-C-G		not specified	Uncertain significance (Feb 06, 2024)
7-129225197-A-T		not specified	Uncertain significance (Aug 04, 2023)
7-129225245-G-T		not specified	Uncertain significance (Nov 10, 2022)
7-129225249-A-C		not specified	Uncertain significance (Sep 16, 2021)
7-129225254-C-T		not specified	Uncertain significance (Sep 16, 2021)
7-129225261-T-G		not specified	Uncertain significance (Aug 13, 2021)
7-129225269-C-T		not specified	Uncertain significance (Nov 03, 2022)
7-129225306-C-T		not specified	Uncertain significance (Oct 29, 2021)
7-129225371-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-129379655-C-G		not specified	Uncertain significance (May 30, 2023)
7-129379689-A-G		not specified	Uncertain significance (May 05, 2023)
7-129389056-C-T		not specified	Uncertain significance (May 17, 2023)
7-129389106-C-G		not specified	Uncertain significance (Mar 01, 2024)
7-129389122-A-G		not specified	Uncertain significance (Sep 06, 2022)
7-129397232-A-G		not specified	Uncertain significance (May 22, 2023)
7-129397321-A-C		not specified	Uncertain significance (Mar 24, 2023)
7-129403413-T-C		not specified	Uncertain significance (Mar 12, 2024)
7-129403466-A-G		not specified	Uncertain significance (Apr 11, 2023)
7-129405126-T-A		not specified	Uncertain significance (Mar 06, 2023)
7-129409493-T-C		not specified	Uncertain significance (Oct 05, 2023)
7-129422865-C-T		not specified	Uncertain significance (Aug 08, 2022)
7-129422919-G-A		not specified	Uncertain significance (Jul 12, 2023)
7-129424889-C-T		not specified	Uncertain significance (Jun 06, 2023)
7-129424925-A-G		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AHCYL2	protein_coding	protein_coding	ENST00000325006	17	205189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00873	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	183	321	0.570	0.0000163	3948
Missense in Polyphen		41	116.16	0.35295		1431
Synonymous	0.497	107	114	0.941	0.00000546	1183
Loss of Function	4.81	5	36.3	0.138	0.00000196	412

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the electrogenic sodium/bicarbonate cotransporter SLC4A4 activity and Mg(2+)-sensitivity. On the contrary of its homolog AHCYL1, does not regulate ITPR1 sensitivity to inositol 1,4,5-trisphosphate (PubMed:19220705). {ECO:0000250|UniProtKB:A6QLP2, ECO:0000269|PubMed:19220705}.
• Pathway: Cysteine and methionine metabolism - Homo sapiens (human);One Carbon Metabolism;Trans-sulfuration and one carbon metabolism;methionine degradation;Methionine Cysteine metabolism;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Bicarbonate transporters;cysteine biosynthesis;superpathway of methionine degradation (Consensus)

Recessive Scores

• pRec: 0.184

Intolerance Scores

• loftool: 0.637
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.648
• hipred: Y
• hipred_score: 0.613
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.863

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ahcyl2

Gene ontology

• Biological process: one-carbon metabolic process;S-adenosylmethionine cycle
• Cellular component: endoplasmic reticulum;cytosol;neuron projection
• Molecular function: adenosylhomocysteinase activity;protein binding