CFDP1

craniofacial development protein 1

Basic information

Region (hg38): 16:75293697-75433503

Links

ENSG00000153774 ∙ NCBI:10428 ∙ OMIM:608108 ∙ HGNC:1873 ∙ Uniprot:Q9UEE9 ∙ 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 CFDP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFDP1 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				5		5
missense			15	2		17
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	7	0

Variants in CFDP1

This is a list of pathogenic ClinVar variants found in the CFDP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-75294039-G-C		CFDP1-related disorder	Uncertain significance (Jul 18, 2023)
16-75305028-C-T		not specified	Uncertain significance (Oct 02, 2023)
16-75305036-C-A		not specified	Uncertain significance (Apr 26, 2023)
16-75305107-C-T		CFDP1-related disorder	Likely benign (Sep 03, 2022)
16-75305108-T-C		not specified	Uncertain significance (Nov 14, 2023)
16-75395093-G-A		not specified	Uncertain significance (May 10, 2022)
16-75395098-G-A		CFDP1-related disorder	Likely benign (Oct 28, 2019)
16-75395112-G-A		not specified	Uncertain significance (May 14, 2024)
16-75395118-C-G		not specified	Uncertain significance (Sep 01, 2021)
16-75395132-G-A		not specified	Uncertain significance (Mar 20, 2024)
16-75395141-T-G		not specified	Uncertain significance (Sep 16, 2021)
16-75395185-T-C			Likely benign (Jul 01, 2022)
16-75395193-C-T		not specified	Uncertain significance (Aug 09, 2021)
16-75411930-G-C		not specified	Uncertain significance (May 29, 2024)
16-75412537-T-C		not specified	Uncertain significance (Feb 27, 2023)
16-75412612-T-C		not specified	Uncertain significance (Oct 16, 2023)
16-75412645-T-C		not specified	Uncertain significance (Dec 26, 2023)
16-75412660-C-A		not specified	Uncertain significance (Jan 23, 2023)
16-75412667-T-C		CFDP1-related disorder	Likely benign (Feb 22, 2021)
16-75412686-C-T		not specified	Uncertain significance (Jan 03, 2024)
16-75412738-C-T		not specified	Uncertain significance (Apr 05, 2023)
16-75414582-C-T		CFDP1-related disorder	Likely benign (May 23, 2019)
16-75414592-C-G		not specified	Uncertain significance (Sep 22, 2023)
16-75414648-C-G		not specified	Uncertain significance (Dec 11, 2023)
16-75433293-C-A		CFDP1-related disorder	Likely benign (Oct 23, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFDP1	protein_coding	protein_coding	ENST00000283882	7	139788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00365	0.988	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.521	168	150	1.12	0.00000705	1971
Missense in Polyphen		46	46.617	0.98676		629
Synonymous	-2.03	74	54.9	1.35	0.00000273	511
Loss of Function	2.32	7	17.4	0.401	8.91e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role during embryogenesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.587
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.692
• hipred: N
• hipred_score: 0.465
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cfdp1

Zebrafish Information Network

• Gene name: cfdp1
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: cell adhesion;multicellular organism development;biological_process;regulation of cell shape;regulation of cell population proliferation;negative regulation of fibroblast apoptotic process
• Cellular component: condensed chromosome kinetochore;cellular_component
• Molecular function: molecular_function