LLCFC1

LLLL and CFNLAS motif containing 1

Basic information

Region (hg38): 7:142939343-142940868

Previous symbols: [ "C7orf34" ]

Links

ENSG00000165131 ∙ NCBI:135927 ∙ OMIM:618946 ∙ HGNC:21750 ∙ Uniprot:Q96L11 ∙ AlphaFold ∙ 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 LLCFC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LLCFC1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in LLCFC1

This is a list of pathogenic ClinVar variants found in the LLCFC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-142940543-C-T		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LLCFC1	protein_coding	protein_coding	ENST00000409607	2	1516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000258	0.339	125683	0	63	125746	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.106	81	78.4	1.03	0.00000388	956
Missense in Polyphen		14	17.832	0.78512		196
Synonymous	0.530	30	33.9	0.884	0.00000194	294
Loss of Function	-0.267	5	4.40	1.14	1.89e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00169	0.00169
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.00169	0.00169
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.93

Haploinsufficiency Scores

• pHI: 0.0829
• hipred: N
• hipred_score: 0.123
• ghis: 0.394

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Llcfc1

Gene ontology

• Cellular component: extracellular region