CASD1

CAS1 domain containing 1

Basic information

Region (hg38): 7:94509219-94557019

Links

ENSG00000127995 ∙ NCBI:64921 ∙ OMIM:611686 ∙ HGNC:16014 ∙ Uniprot:Q96PB1 ∙ 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 CASD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASD1 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	0

Variants in CASD1

This is a list of pathogenic ClinVar variants found in the CASD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-94510109-G-A		not specified	Uncertain significance (Dec 28, 2022)
7-94518223-T-C		not specified	Uncertain significance (Oct 04, 2022)
7-94533211-A-C		not specified	Uncertain significance (Dec 20, 2021)
7-94535312-C-G		not specified	Uncertain significance (Aug 12, 2021)
7-94535317-T-C		not specified	Uncertain significance (May 27, 2022)
7-94535508-A-C		not specified	Uncertain significance (Jul 06, 2021)
7-94535510-C-T		not specified	Uncertain significance (May 01, 2024)
7-94537545-G-A		not specified	Uncertain significance (Aug 08, 2022)
7-94537559-C-T		not specified	Uncertain significance (Apr 09, 2024)
7-94537640-C-T		not specified	Uncertain significance (Jan 04, 2022)
7-94537733-C-A		not specified	Uncertain significance (Nov 30, 2022)
7-94537790-A-G		not specified	Uncertain significance (Jul 14, 2021)
7-94537799-A-G		not specified	Uncertain significance (Aug 08, 2023)
7-94537810-C-G		not specified	Uncertain significance (Apr 08, 2024)
7-94537820-A-G		not specified	Uncertain significance (Dec 28, 2022)
7-94537848-T-C		not specified	Uncertain significance (Jan 03, 2024)
7-94537883-A-G		not specified	Uncertain significance (May 04, 2022)
7-94545581-T-A		not specified	Uncertain significance (Jan 18, 2023)
7-94545608-T-C		not specified	Uncertain significance (Apr 08, 2024)
7-94545635-G-A		not specified	Uncertain significance (Nov 12, 2021)
7-94545647-G-C		not specified	Uncertain significance (Sep 25, 2023)
7-94545698-A-G		not specified	Uncertain significance (Aug 08, 2023)
7-94549547-G-T		not specified	Uncertain significance (Dec 03, 2021)
7-94551339-T-C		not specified	Uncertain significance (Nov 29, 2023)
7-94551362-G-A		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASD1	protein_coding	protein_coding	ENST00000297273	18	47801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0448	0.955	125697	0	21	125718	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	294	405	0.725	0.0000197	5248
Missense in Polyphen		86	163.79	0.52507		2115
Synonymous	0.214	134	137	0.977	0.00000676	1434
Loss of Function	4.42	11	41.9	0.263	0.00000190	557

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: O-acetyltransferase that catalyzes 9-O-acetylation of sialic acids (PubMed:20947662, PubMed:26169044). Sialic acids are sugars at the reducing end of glycoproteins and glycolipids, and are involved in various processes such as cell-cell interactions, host-pathogen recognition (PubMed:20947662, PubMed:26169044). {ECO:0000269|PubMed:26169044, ECO:0000305|PubMed:20947662}.

Intolerance Scores

• loftool: 0.715
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.63

Haploinsufficiency Scores

• pHI: 0.330
• hipred: Y
• hipred_score: 0.704
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.287

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Casd1

Gene ontology

• Biological process: carbohydrate metabolic process
• Cellular component: Golgi apparatus;integral component of Golgi membrane
• Molecular function: acetyltransferase activity;N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity