FAHD2A

fumarylacetoacetate hydrolase domain containing 2A

Basic information

Region (hg38): 2:95402708-95416616

Links

ENSG00000115042 ∙ NCBI:51011 ∙ ∙ HGNC:24252 ∙ Uniprot:Q96GK7 ∙ 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 FAHD2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAHD2A 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				2		2
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in FAHD2A

This is a list of pathogenic ClinVar variants found in the FAHD2A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-95405577-A-G		not specified	Uncertain significance (Dec 08, 2023)
2-95405602-A-G		not specified	Uncertain significance (Feb 08, 2025)
2-95405634-G-T		not specified	Uncertain significance (Apr 12, 2022)
2-95405666-C-G		not specified	Uncertain significance (Aug 09, 2021)
2-95405706-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-95405710-G-A		not specified	Uncertain significance (Mar 07, 2024)
2-95405753-G-A			Likely benign (Feb 01, 2025)
2-95405757-A-G		not specified	Uncertain significance (Jun 22, 2021)
2-95405771-G-A			Likely benign (May 01, 2022)
2-95405782-C-G		not specified	Uncertain significance (Oct 03, 2023)
2-95406963-G-C		not specified	Uncertain significance (Dec 06, 2022)
2-95406972-C-T		not specified	Uncertain significance (Mar 04, 2024)
2-95406973-G-A		not specified	Uncertain significance (Jan 18, 2025)
2-95406991-T-G		not specified	Uncertain significance (Oct 27, 2022)
2-95406997-C-T		not specified	Uncertain significance (May 09, 2024)
2-95407003-C-T		not specified	Uncertain significance (Jan 20, 2025)
2-95407006-G-A		not specified	Uncertain significance (Feb 13, 2025)
2-95407012-A-C		not specified	Uncertain significance (Sep 15, 2021)
2-95407023-T-C		not specified	Uncertain significance (Nov 10, 2022)
2-95407035-A-G		not specified	Uncertain significance (May 31, 2023)
2-95407065-G-A		not specified	Uncertain significance (Aug 04, 2024)
2-95407066-T-A		not specified	Uncertain significance (Nov 08, 2022)
2-95407078-A-G		not specified	Uncertain significance (Nov 18, 2022)
2-95407093-T-C		not specified	Uncertain significance (Jun 22, 2021)
2-95407107-A-G		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAHD2A	protein_coding	protein_coding	ENST00000233379	7	13896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000135	0.624	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.328	171	183	0.932	0.00000995	2038
Missense in Polyphen		58	65.283	0.88844		757
Synonymous	-0.127	74	72.6	1.02	0.00000414	640
Loss of Function	0.995	11	15.2	0.725	8.29e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000273	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000217	0.000217
South Asian	0.000295	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have hydrolase activity. {ECO:0000250}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.432
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.218
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00689

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fahd2a
• Phenotype: growth/size/body region phenotype; skeleton phenotype

Gene ontology

• Molecular function: hydrolase activity;metal ion binding