Is EFCAB13 p.Ser894= (c.2682C>T) pathogenic?

EFCAB13 p.Ser894= (c.2682C>T) is classified Benign in EFCAB13 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-20). Rare (popmax 0.954%, amr); Associated with EFCAB13-related disorder.

What condition is associated with EFCAB13 p.Ser894= (c.2682C>T)?

EFCAB13 p.Ser894= (c.2682C>T) is associated with EFCAB13-related disorder (ClinVar).

How common is EFCAB13 p.Ser894= (c.2682C>T) in the general population?

EFCAB13 p.Ser894= (c.2682C>T) is rare (popmax 0.954%, amr) (gnomAD).

EFCAB13 p.Ser894=

c.2682C>T · rs200910398 · VCV3034231

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.954%, amr)

Conditions

EFCAB13-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.24	acceptor loss, 43 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -4.7
Overall
CADD	0.093	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.954% Admixed American · 555/58,192 alleles

Filtering AF 0.888% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.862%

Overall 0.0562% 902/1,605,002 alleles · rare exomes 761/1,452,964 · genomes 141/152,038 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.954%	105
Middle Eastern	0.167%	599
Ashkenazi Jewishnot grpmax-eligible	0.106%	943
Remaining individualsnot grpmax-eligible	0.0918%	1,090
European (non-Finnish)	0.0189%	5,278
East Asian	0.0157%	6,363
African / African-American	0.0121%	8,292
South Asian	0.0113%	8,865

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.Ser894=
Coding: c.2682C>T
MANE Select: NM_152347
dbSNP: rs200910398
Type: single nucleotide variant
Location: chr17:47440474 (GRCh38)
Gene constraint: LOEUF 0.953 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
Structure: AlphaFold pLDDT 53.37
Residue 894: the ef-hand 6 domain

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

Disease context

EFCAB13-related disorder

Similar variants

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
EFCAB13 p.Asp611Asn 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-ser894 (accessed [today's date]).

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