CSAD

cysteine sulfinic acid decarboxylase

Basic information

Region (hg38): 12:53157663-53180925

Links

ENSG00000139631 ∙ NCBI:51380 ∙ OMIM:616569 ∙ HGNC:18966 ∙ Uniprot:Q9Y600 ∙ 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 CSAD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSAD 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				1	3	4
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding						0
Total	0	0	26	1	3

Variants in CSAD

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

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

Position	Type	Phenotype	Significance	ClinVar
12-53158530-C-T		not specified	Uncertain significance (Jun 27, 2023)
12-53158546-G-A		not specified	Uncertain significance (Oct 20, 2021)
12-53158549-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-53158552-A-T		not specified	Uncertain significance (Jun 06, 2023)
12-53158588-C-G		not specified	Uncertain significance (Aug 02, 2021)
12-53158612-G-A		not specified	Uncertain significance (Aug 28, 2024)
12-53158648-C-T		not specified	Uncertain significance (Sep 28, 2022)
12-53158668-T-C		not specified	Uncertain significance (Mar 29, 2023)
12-53158674-A-C		not specified	Uncertain significance (Dec 13, 2022)
12-53158680-G-A		not specified	Uncertain significance (Aug 12, 2024)
12-53159625-T-C		not specified	Uncertain significance (Jun 30, 2022)
12-53159666-C-T		not specified	Uncertain significance (Nov 25, 2024)
12-53159675-G-C		not specified	Uncertain significance (Oct 06, 2021)
12-53159676-G-C		not specified	Uncertain significance (Aug 17, 2021)
12-53159676-G-T		not specified	Uncertain significance (Feb 10, 2022)
12-53159679-G-A		not specified	Uncertain significance (Apr 14, 2022)
12-53159681-A-T		not specified	Uncertain significance (Oct 26, 2022)
12-53159938-C-T		not specified	Likely benign (Mar 07, 2024)
12-53160121-G-A		not specified	Uncertain significance (Apr 20, 2024)
12-53160147-C-T		not specified	Uncertain significance (Jun 21, 2023)
12-53160172-G-C		not specified	Uncertain significance (Sep 03, 2024)
12-53160200-A-C		not specified	Uncertain significance (Sep 04, 2024)
12-53160240-G-A		not specified	Uncertain significance (Dec 04, 2024)
12-53160300-T-C		not specified	Uncertain significance (Mar 31, 2022)
12-53160306-C-T		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSAD	protein_coding	protein_coding	ENST00000267085	16	23689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.08e-12	0.608	125572	0	176	125748	0.000700

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.384	299	318	0.939	0.0000196	3346
Missense in Polyphen		115	140.49	0.81858		1550
Synonymous	1.46	107	128	0.835	0.00000739	1060
Loss of Function	1.47	22	30.8	0.714	0.00000140	344

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00228	0.00228
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000281	0.000277
European (Non-Finnish)	0.000802	0.000800
Middle Eastern	0.000272	0.000272
South Asian	0.000654	0.000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the decarboxylation of L-aspartate, 3-sulfino- L-alanine (cysteine sulfinic acid), and L-cysteate to beta- alanine, hypotaurine and taurine, respectively. The preferred substrate is 3-sulfino-L-alanine. Does not exhibit any decarboxylation activity toward glutamate. {ECO:0000250|UniProtKB:Q9DBE0}.
• Pathway: Taurine and hypotaurine metabolism - Homo sapiens (human);Taurine and Hypotaurine Metabolism;Trans-sulfuration pathway;One carbon metabolism and related pathways;taurine biosynthesis;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;Metabolism;Methionine Cysteine metabolism;Sulfur amino acid metabolism (Consensus)

Recessive Scores

• pRec: 0.260

Intolerance Scores

• loftool: 0.879
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.237
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csad
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: csad
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: L-cysteine catabolic process to hypotaurine;L-cysteine catabolic process to taurine;taurine biosynthetic process
• Cellular component: cytoplasm
• Molecular function: aspartate 1-decarboxylase activity;sulfinoalanine decarboxylase activity;pyridoxal phosphate binding