Is EFCAB13 p.Phe797= (c.2391C>T) pathogenic?

EFCAB13 p.Phe797= (c.2391C>T) is classified Benign in EFCAB13 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-15). Common (popmax 34.2%, eas) — too common for a highly-penetrant pathogenic allele; Associated with EFCAB13-related disorder.

What condition is associated with EFCAB13 p.Phe797= (c.2391C>T)?

EFCAB13 p.Phe797= (c.2391C>T) is associated with EFCAB13-related disorder (ClinVar).

EFCAB13 p.Phe797=

Q: How common is EFCAB13 p.Phe797= (c.2391C>T) in the general population?

EFCAB13 p.Phe797= (c.2391C>T) is common (popmax 34.2%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2391C>T · rs3883318 · VCV3059807

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 34.2%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

EFCAB13-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.84
Overall
CADD	1.449	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 34.2% East Asian · 15,320/44,794 alleles

Filtering AF 33.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 33.6%

Overall 8.48% 136,882/1,613,460 alleles · common exomes 123,485/1,461,258 · genomes 13,397/152,202 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	34.2%	3
South Asian	18%	6
Amishnot grpmax-eligible	14.3%	7
Admixed American	11%	9
Ashkenazi Jewishnot grpmax-eligible	10.4%	10
Middle Eastern	10.1%	10
Remaining individualsnot grpmax-eligible	9.44%	11
African / African-American	6.92%	14
European (non-Finnish)	6.82%	15
Finnishnot grpmax-eligible	5%	20

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: EFCAB13
Protein: p.Phe797=
Coding: c.2391C>T
MANE Select: NM_152347
dbSNP: rs3883318
Type: single nucleotide variant
Location: chr17:47412885 (GRCh38)
Gene constraint: LOEUF 0.953 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
Structure: AlphaFold pLDDT 53.37
Residue 797: the ef-hand 5 domain

Full EFCAB13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EFCAB13-related disorder

Similar variants

EFCAB13 p.Phe797Val Uncertain significance ★ ⚠ same residue
EFCAB13 c.1802-9A>G Likely benign same condition
EFCAB13 c.806-1G>A Benign same condition
EFCAB13 p.Arg211Ter Benign same condition
EFCAB13 p.Arg236Ter Benign same condition
EFCAB13 p.Asn805= Benign same condition
EFCAB13 p.Asn968= Benign same condition
EFCAB13 p.Asp541Val Benign ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/efcab13-p-phe797 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown