ACCSL

protein-coding

1-aminocyclopropane-1-carboxylate synthase homolog (inactive) like

Gene summary

Predicted to enable transaminase activity. Predicted to be involved in amino acid metabolic process. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001031854.2

Inheritance

—

ClinVar variants

U:82B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr11:44,047,981-44,059,977

External References & Databases

Ensembl (ENSG00000205126)

Transcript & Mutation Effects

hg38 • Region Span ~12.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ACCSL variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031854.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			80 clinvar	5 clinvar		85
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	82	6	0	88

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031854.2	RefSeq	NP_001027025.2	14	MANE Select
ENST00000378832.1	Ensembl	ENSP00000368109.1	14	MANE Select
NM_001363113.1	RefSeq	NP_001350042.1	13	Standard
ENST00000527145.1	Ensembl	ENSP00000436505.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biosynthetic process

Molecular Function

catalytic activity
pyridoxal phosphate binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378832
Coding exons: 14
Length: 11997
Individuals with no LoFs: 124720
Homozygous LoFs: 0
Heterozygous LoFs: 93
Defined: 124813
p: 0.000373

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.264	304	317	0.958	0.0000178	3743
Missense (PolyPhen)		64	77.582	0.82493		1105
Synonymous	-0.921	133	120	1.11	0.00000602	1091
Loss of Function	0.226	27	28.3	0.954	0.00000137	339

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00095	0.00095	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00037	0.00037	rare
South Asian	0.00046	0.00046	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.547
RVIS EVS: -0.15
RVIS percentile EVS: 42.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00916

Gene Damage Prediction

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