LKAAEAR1

Gene

LKAAEAR motif containing 1

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C20orf201

MANE transcript

NM_001353425.2

Inheritance

—

ClinVar variants

U:36B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1

Max pathogenic AF

—

Genomic locus

chr20:64,083,376-64,084,398

External References & Databases

Ensembl (ENSG00000171695)

Transcript & Mutation Effects

hg38 • Region Span ~1.0 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 LKAAEAR1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 47

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001353425.2. 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						0
missense			36 clinvar	2 clinvar		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	2	0	38

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001353425.2	RefSeq	NP_001340354.1	3	MANE Select
ENST00000302096.5	Ensembl	ENSP00000302763.4	3	MANE Select
NM_001007125.3	RefSeq	NP_001007126.1	2	Standard
NM_001386971.1	RefSeq	NP_001373900.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308906
Coding exons: 2
Length: 980
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.528	73	86.8	0.841	0.00000411	1417
Missense (PolyPhen)		15	22.481	0.66723		410
Synonymous	0.529	36	40.3	0.894	0.00000200	547
Loss of Function	0.00603	2	2.01	0.995	9.05e-8	46

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (gene trap): N