CMAS

cytidine monophosphate N-acetylneuraminic acid synthetase

Basic information

Region (hg38): 12:22046218-22065674

Links

ENSG00000111726 ∙ NCBI:55907 ∙ OMIM:603316 ∙ HGNC:18290 ∙ Uniprot:Q8NFW8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CMAS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMAS 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	1	3
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	14	3	2

Variants in CMAS

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

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

Position	Type	Phenotype	Significance	ClinVar
12-22046311-C-T		not specified	Uncertain significance (Sep 21, 2021)
12-22046356-G-T		not specified	Uncertain significance (Feb 28, 2024)
12-22046381-G-A			Benign (Jan 30, 2018)
12-22046433-C-T		not specified	Uncertain significance (Feb 12, 2024)
12-22046464-G-A		not specified	Uncertain significance (Jun 29, 2023)
12-22046552-G-A			Likely benign (May 01, 2023)
12-22055268-T-C		not specified	Uncertain significance (Jul 20, 2021)
12-22055532-A-G		not specified	Uncertain significance (Dec 17, 2023)
12-22055574-C-T		not specified	Uncertain significance (Jun 09, 2022)
12-22058680-A-G		not specified	Uncertain significance (Sep 25, 2023)
12-22060860-G-A		not specified	Uncertain significance (Oct 24, 2023)
12-22060872-G-T		not specified	Uncertain significance (Mar 20, 2024)
12-22060881-T-C		not specified	Uncertain significance (Jul 14, 2023)
12-22060923-T-C		not specified	Uncertain significance (Dec 21, 2022)
12-22062302-G-C		not specified	Uncertain significance (Aug 02, 2021)
12-22062349-G-A		not specified	Uncertain significance (May 20, 2024)
12-22062440-T-TATC			Benign (Aug 16, 2018)
12-22065172-C-T		not specified	Likely benign (May 17, 2023)
12-22065180-G-A		not specified	Uncertain significance (Aug 07, 2023)
12-22065202-A-G		not specified	Uncertain significance (Jan 10, 2022)
12-22065215-C-T			Benign/Likely benign (Oct 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMAS	protein_coding	protein_coding	ENST00000229329	8	19501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.561	0.439	125724	0	20	125744	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	125	229	0.545	0.0000115	2791
Missense in Polyphen		25	70.472	0.35475		826
Synonymous	1.03	71	82.9	0.856	0.00000392	851
Loss of Function	3.62	5	24.3	0.206	0.00000146	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000544
Finnish	0.000370	0.000370
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000556	0.0000544
South Asian	0.0000670	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the activation of N-acetylneuraminic acid (NeuNAc) to cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-NeuNAc), a substrate required for the addition of sialic acid. Has some activity toward NeuNAc, N-glycolylneuraminic acid (Neu5Gc) or 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN).
• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;Aminosugars metabolism;Post-translational protein modification;Metabolism of proteins;CMP-<i>N</i>-acetylneuraminate biosynthesis I (eukaryotes);Aminosugars metabolism;Sialic acid metabolism;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.247
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.365
• hipred: Y
• hipred_score: 0.685
• ghis: 0.674

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.915

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmas

Gene ontology

• Biological process: N-acetylneuraminate metabolic process
• Cellular component: nucleus;nucleoplasm;membrane
• Molecular function: N-acylneuraminate cytidylyltransferase activity