EFCAB2

EF-hand calcium binding domain 2, the group of Dynein regulatory complex|EF-hand domain containing|Cilia and flagella associated

Basic information

Region (hg38): 1:244969681-245127164

Links

ENSG00000203666 ∙ NCBI:84288 ∙ OMIM:619617 ∙ HGNC:28166 ∙ Uniprot:Q5VUJ9 ∙ 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 EFCAB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB2 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					1	1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in EFCAB2

This is a list of pathogenic ClinVar variants found in the EFCAB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-244970434-G-A		not specified	Uncertain significance (Nov 09, 2021)
1-244970434-G-T		not specified	Uncertain significance (Jul 26, 2022)
1-245017253-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-245017322-G-C		not specified	Uncertain significance (Dec 21, 2023)
1-245082118-C-T			Benign (May 08, 2018)
1-245087293-T-C		not specified	Uncertain significance (Sep 27, 2021)
1-245087326-A-T		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB2	protein_coding	protein_coding	ENST00000366523	7	157460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.92e-7	0.262	125685	0	48	125733	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.254	90	83.5	1.08	0.00000416	1061
Missense in Polyphen		15	20.575	0.72906		303
Synonymous	-0.635	31	26.8	1.16	0.00000140	271
Loss of Function	0.247	10	10.9	0.919	5.91e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000107	0.0000924
European (Non-Finnish)	0.000295	0.000290
Middle Eastern	0.000110	0.000109
South Asian	0.000232	0.000196
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the nexin-dynein regulatory complex (N- DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. {ECO:0000250|UniProtKB:A8J3A0}.

Intolerance Scores

• loftool: 0.697
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.197
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0857

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcab2

Gene ontology

• Cellular component: cytoplasm;cytoskeleton;motile cilium
• Molecular function: calcium ion binding