FAHD1

fumarylacetoacetate hydrolase domain containing 1

Basic information

Region (hg38): 16:1826966-1840207

Previous symbols: [ "C16orf36" ]

Links

ENSG00000180185 ∙ NCBI:81889 ∙ OMIM:616320 ∙ HGNC:14169 ∙ Uniprot:Q6P587 ∙ 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 FAHD1 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAHD1 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			17			17
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding		1	7		1	9
Total	1	1	24	0	1

Highest pathogenic variant AF is 0.000112

Variants in FAHD1

This is a list of pathogenic ClinVar variants found in the FAHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1827407-C-A		not specified	Uncertain significance (Oct 26, 2021)
16-1827410-A-G		not specified	Uncertain significance (Oct 25, 2023)
16-1827422-A-C		not specified	Uncertain significance (Dec 16, 2023)
16-1827425-C-T		not specified	Uncertain significance (Sep 27, 2021)
16-1827469-G-C		not specified	Uncertain significance (Dec 23, 2022)
16-1827483-T-A		not specified	Uncertain significance (Aug 02, 2023)
16-1827528-G-C		not specified	Uncertain significance (Mar 01, 2023)
16-1827552-T-C		not specified	Uncertain significance (Oct 17, 2023)
16-1827594-C-A		not specified	Uncertain significance (Feb 16, 2023)
16-1827617-C-T		not specified	Uncertain significance (Jun 03, 2022)
16-1827737-C-T		not specified	Uncertain significance (Sep 14, 2023)
16-1827746-A-C		not specified	Uncertain significance (May 30, 2024)
16-1827746-A-G		not specified	Uncertain significance (May 02, 2024)
16-1827753-A-G		not specified	Uncertain significance (Nov 29, 2021)
16-1827771-C-G		not specified	Uncertain significance (Oct 25, 2022)
16-1827783-G-A		not specified	Uncertain significance (Mar 25, 2024)
16-1827783-G-T		not specified	Uncertain significance (Dec 07, 2021)
16-1827815-G-A		not specified	Uncertain significance (Feb 16, 2023)
16-1827848-G-A		not specified	Uncertain significance (Nov 14, 2023)
16-1827852-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-1834265-T-G		not specified	Uncertain significance (Sep 22, 2023)
16-1834352-G-T		not specified	Uncertain significance (Jul 29, 2023)
16-1834363-C-G		not specified	Uncertain significance (Feb 14, 2023)
16-1834363-C-T		not specified	Uncertain significance (Feb 21, 2024)
16-1834371-G-A			Benign (Jul 19, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAHD1	protein_coding	protein_coding	ENST00000382666	2	13241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.95e-12	0.00240	125621	0	108	125729	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.84	198	137	1.44	0.00000630	1599
Missense in Polyphen		51	40.938	1.2458		469
Synonymous	-1.71	76	59.3	1.28	0.00000293	509
Loss of Function	-2.29	14	7.32	1.91	3.11e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00247	0.00246
Ashkenazi Jewish	0.00	0.00
East Asian	0.00115	0.00114
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.00115	0.00114
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable mitochondrial acylpyruvase which is able to hydrolyze acetylpyruvate and fumarylpyruvate in vitro (PubMed:15551868, PubMed:21878618). Also has oxaloacetate decarboxylase activity (PubMed:25575590). {ECO:0000269|PubMed:15551868, ECO:0000269|PubMed:21878618, ECO:0000269|PubMed:25575590}.
• Pathway: Tyrosine metabolism - Homo sapiens (human);Citric acid cycle (TCA cycle);Pyruvate metabolism and Citric Acid (TCA) cycle;The citric acid (TCA) cycle and respiratory electron transport;Metabolism (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.254
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.177
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.879

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fahd1

Gene ontology

• Biological process: tricarboxylic acid cycle
• Cellular component: nucleoplasm;mitochondrion;mitochondrial matrix;cytosol
• Molecular function: oxaloacetate decarboxylase activity;acetylpyruvate hydrolase activity;fumarylpyruvate hydrolase activity;metal ion binding;acylpyruvate hydrolase activity