CKLF-CMTM1

protein-coding

CKLF-CMTM1 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring CKLF (chemokine-like factor) and CMTM1 (CKLF-like MARVEL transmembrane domain containing 1) genes on chromosome 16. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Feb 2011]

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:2

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr16:66,552,587-66,579,135

External References & Databases

Ensembl (ENSG00000254788)

NCBI Gene (100529251)

Transcript & Mutation Effects

hg38 • Region Span ~26.5 kb

Loading mutation effect viewer...

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 CKLF-CMTM1 variants in ClinVar

2 Conditions Cataloged

Inborn genetic diseasesTotal: 15

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

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

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001202509.2	RefSeq	NP_001189438.1	3	Standard
NM_001204098.2	RefSeq	NP_001191027.1	4	Standard
NM_001204099.2	RefSeq	NP_001191028.1	4	Standard
ENST00000527729.5	Ensembl	ENSP00000433998.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000527729
Coding exons: 3
Length: 26549
Individuals with no LoFs: 123777
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 123781
p: 0.0000162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.101	75	72.6	1.03	0.00000397	748
Missense (PolyPhen)		18	18.034	0.99812		195
Synonymous	0.465	30	33.4	0.898	0.00000228	230
Loss of Function	0.334	2	2.58	0.776	1.09e-7	31

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000091	0.000091	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000089	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.28
RVIS percentile EVS: 71.08

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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