Is CRAT p.Arg623fs (c.1867del) pathogenic?

CRAT p.Arg623fs (c.1867del) is classified Uncertain significance in CRAT (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-01). Absent from gnomAD.

How common is CRAT p.Arg623fs (c.1867del) in the general population?

CRAT p.Arg623fs (c.1867del) is absent from gnomAD (gnomAD).

CRAT p.Arg623fs

c.1867del · rs2131428918 · VCV1176289

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	escapes	premature termination codon in the last exon (14 of 14) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.41	GERP -0.41, phastCons 0.22

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: CRAT
Protein: p.Arg623fs
Coding: c.1867del
MANE Select: NM_000755
dbSNP: rs2131428918
Type: Deletion
Location: chr9:129095411 (GRCh38)
Gene constraint: LOEUF 1.111 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.75 · 3 PDB

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

Similar variants

CRAT p.Arg623Gln Uncertain significance ★★ ⚠ same residue
CRAT p.Arg623Trp Uncertain significance ★ ⚠ same residue
CRAT p.Lys166fs Likely pathogenic ★ same type
CRAT c.1464+306_1527+181del Uncertain significance ★ same type
CRAT c.1665+5_1665+9del Uncertain significance ★ same type
CRAT c.805+5_805+7del Uncertain significance ★ same type
CRAT p.Ala440fs Uncertain significance ★ same type
CRAT p.Asp298fs Uncertain significance ★ 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/crat-p-arg623fs (accessed [today's date]).

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