ASPHD2

aspartate beta-hydroxylase domain containing 2

Basic information

Region (hg38): 22:26429259-26445015

Links

ENSG00000128203 ∙ NCBI:57168 ∙ ∙ HGNC:30437 ∙ Uniprot:Q6ICH7 ∙ 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 ASPHD2 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASPHD2 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in ASPHD2

This is a list of pathogenic ClinVar variants found in the ASPHD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-26433641-C-T		not specified	Uncertain significance (May 16, 2022)
22-26433724-T-C		not specified	Uncertain significance (Dec 19, 2023)
22-26433772-G-A		not specified	Uncertain significance (Dec 01, 2022)
22-26433865-C-T		not specified	Uncertain significance (Sep 16, 2021)
22-26433880-G-A		not specified	Uncertain significance (Jul 20, 2022)
22-26433950-A-C		not specified	Uncertain significance (Jan 08, 2024)
22-26433961-T-G		not specified	Uncertain significance (Oct 21, 2021)
22-26433998-A-C		not specified	Uncertain significance (Apr 14, 2023)
22-26434072-G-T			Uncertain significance (Jan 12, 2024)
22-26434091-G-A		not specified	Uncertain significance (Jul 26, 2022)
22-26434283-C-A		not specified	Uncertain significance (Aug 02, 2023)
22-26434300-T-G		not specified	Likely benign (Jul 05, 2023)
22-26434304-C-T		not specified	Uncertain significance (Nov 09, 2023)
22-26434354-T-G		not specified	Uncertain significance (Aug 02, 2023)
22-26434355-G-A		not specified	Uncertain significance (Dec 21, 2023)
22-26434406-A-G		not specified	Uncertain significance (Oct 05, 2023)
22-26434424-G-A		not specified	Uncertain significance (Sep 20, 2023)
22-26443105-G-C		not specified	Uncertain significance (Apr 28, 2022)
22-26443115-C-T		not specified	Uncertain significance (Dec 19, 2023)
22-26443117-C-T		not specified	Uncertain significance (Aug 21, 2023)
22-26443118-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASPHD2	protein_coding	protein_coding	ENST00000215906	3	15743

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.459	0.540	125712	0	35	125747	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	166	250	0.663	0.0000172	2393
Missense in Polyphen		58	115.79	0.50091		1038
Synonymous	-1.30	130	113	1.16	0.00000826	757
Loss of Function	2.78	3	14.3	0.209	6.95e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000918	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00116	0.00116
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000164	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as 2-oxoglutarate-dependent dioxygenase. {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.323
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.163
• hipred: Y
• hipred_score: 0.740
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asphd2

Gene ontology

• Biological process: peptidyl-aspartic acid hydroxylation;oxidation-reduction process
• Cellular component: membrane;integral component of membrane
• Molecular function: peptide-aspartate beta-dioxygenase activity;metal ion binding