CKLF-CMTM1

CKLF-CMTM1 readthrough

Basic information

Region (hg38): 16:66552587-66579135

Links

ENSG00000254788 ∙ NCBI:100529251 ∙ ∙ HGNC:39977 ∙ ∙ ∙ 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 CKLF-CMTM1 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKLF-CMTM1 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			11	2	1	14
Total	0	0	13	2	1

Variants in CKLF-CMTM1

This is a list of pathogenic ClinVar variants found in the CKLF-CMTM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66552728-C-A		not specified	Likely benign (Dec 21, 2023)
16-66558277-A-G		not specified	Uncertain significance (May 02, 2024)
16-66563170-G-A		not specified	Uncertain significance (Jul 08, 2021)
16-66563192-C-A		not specified	Uncertain significance (Jun 24, 2022)
16-66565890-T-C		not specified	Uncertain significance (Jul 05, 2022)
16-66565923-A-G		not specified	Uncertain significance (Mar 25, 2024)
16-66565924-C-G		not specified	Uncertain significance (Nov 17, 2023)
16-66565925-G-A		not specified	Uncertain significance (Aug 05, 2024)
16-66565940-C-G		not specified	Uncertain significance (Oct 04, 2024)
16-66565987-G-A			Benign (Dec 31, 2019)
16-66566526-C-T		not specified	Uncertain significance (Jun 05, 2023)
16-66566599-G-A		not specified	Uncertain significance (Oct 20, 2024)
16-66566607-A-G		not specified	Uncertain significance (Jan 08, 2024)
16-66566676-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-66566688-C-T		not specified	Uncertain significance (Oct 12, 2024)
16-66566692-G-C		not specified	Likely benign (Dec 05, 2022)
16-66566709-G-A		not specified	Likely benign (Aug 02, 2021)
16-66566742-C-G		not specified	Uncertain significance (Oct 04, 2024)
16-66566769-C-G		not specified	Uncertain significance (Apr 27, 2023)
16-66566772-C-T		not specified	Uncertain significance (Mar 15, 2024)
16-66566794-C-T		not specified	Uncertain significance (May 13, 2024)
16-66566796-A-G		not specified	Uncertain significance (Mar 01, 2023)
16-66566838-G-A		not specified	Uncertain significance (May 24, 2024)
16-66566888-G-T		not specified	Uncertain significance (Mar 29, 2023)
16-66566911-T-C		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKLF-CMTM1	protein_coding	protein_coding	ENST00000527729	3	26549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0346	0.638	123777	0	4	123781	0.0000162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.101	75	72.6	1.03	0.00000397	748
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000887	0.00000887
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.182
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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