Is EFHC1 p.Asp167fs (c.499del) pathogenic?

EFHC1 p.Asp167fs (c.499del) is classified Uncertain significance in EFHC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-11-15). Absent from gnomAD.

How common is EFHC1 p.Asp167fs (c.499del) in the general population?

EFHC1 p.Asp167fs (c.499del) is absent from gnomAD (gnomAD).

EFHC1 p.Asp167fs

c.499del · rs2532587890 · VCV2689001

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP 0.62, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EFHC1
Protein: p.Asp167fs
Coding: c.499del
MANE Select: NM_018100
dbSNP: rs2532587890
Type: Deletion
Location: chr6:52438517 (GRCh38)
Gene constraint: LOEUF 0.906 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.31 · 2 PDB
Residue 167: the dm10 1 domain

Full EFHC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EFHC1 p.Asp228fs Uncertain significance ★★ same type
EFHC1 p.Gln395fs Uncertain significance ★★ same type
EFHC1 p.Ile367fs Uncertain significance ★★ same type
EFHC1 p.Phe438fs Pathogenic ★ same type
EFHC1 p.Asp363fs Uncertain significance ★ same type
EFHC1 p.Glu391fs Uncertain significance ★ same type
EFHC1 p.Ile122_Tyr123del Uncertain significance ★ same type
EFHC1 c.1138-293del Benign ★ same type

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/efhc1-p-asp167fs (accessed [today's date]).

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