ASPHD1

aspartate beta-hydroxylase domain containing 1

Basic information

Region (hg38): 16:29900375-29919864

Links

ENSG00000174939 ∙ NCBI:253982 ∙ ∙ HGNC:27380 ∙ Uniprot:Q5U4P2 ∙ 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 ASPHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASPHD1 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			4	1		5
Total	0	0	24	1	0

Variants in ASPHD1

This is a list of pathogenic ClinVar variants found in the ASPHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-29900991-G-A		not specified	Uncertain significance (Jun 28, 2022)
16-29900997-G-T		not specified	Uncertain significance (Jul 15, 2021)
16-29901035-C-G		not specified	Uncertain significance (Sep 20, 2023)
16-29901076-G-C		not specified	Uncertain significance (Jul 14, 2021)
16-29901279-T-C		not specified	Uncertain significance (Aug 08, 2023)
16-29901318-G-T		not specified	Uncertain significance (Dec 15, 2023)
16-29901441-A-C		not specified	Uncertain significance (Aug 21, 2023)
16-29901567-C-G		not specified	Uncertain significance (Dec 19, 2022)
16-29901638-G-A		not specified	Uncertain significance (Jul 25, 2023)
16-29901678-C-G		not specified	Uncertain significance (Sep 22, 2023)
16-29901683-C-T		not specified	Uncertain significance (Apr 13, 2022)
16-29901716-T-G		not specified	Uncertain significance (Jun 06, 2023)
16-29901773-T-C		not specified	Uncertain significance (Apr 28, 2022)
16-29901799-G-C		not specified	Uncertain significance (Sep 21, 2023)
16-29901864-G-C		not specified	Uncertain significance (Sep 01, 2021)
16-29905796-G-A		not specified	Uncertain significance (Feb 28, 2024)
16-29905803-G-A		not specified	Uncertain significance (Jan 09, 2024)
16-29905822-C-G		not specified	Uncertain significance (Jan 20, 2023)
16-29905859-C-T		not specified	Uncertain significance (Nov 21, 2022)
16-29905891-C-A		not specified	Uncertain significance (Aug 12, 2021)
16-29906951-C-T		not specified	Uncertain significance (Feb 09, 2022)
16-29907038-G-A		not specified	Uncertain significance (Mar 25, 2024)
16-29907047-G-A		not specified	Uncertain significance (Jul 05, 2023)
16-29907071-AG-A		not specified	Uncertain significance (May 04, 2022)
16-29911050-G-A		KCTD13-related disorder	Likely benign (Apr 03, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASPHD1	protein_coding	protein_coding	ENST00000308748	3	19490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00224	0.928	125733	0	12	125745	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	184	241	0.765	0.0000149	2440
Missense in Polyphen		54	83.818	0.64426		779
Synonymous	1.44	84	103	0.819	0.00000640	886
Loss of Function	1.58	6	11.9	0.504	6.33e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000877	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000183	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.528
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.329
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asphd1

Zebrafish Information Network

• Gene name: asphd1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

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