Is CIT p.Val397fs (c.1189del) pathogenic?

CIT p.Val397fs (c.1189del) is classified Pathogenic in CIT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-22). Absent from gnomAD.

How common is CIT p.Val397fs (c.1189del) in the general population?

CIT p.Val397fs (c.1189del) is absent from gnomAD (gnomAD).

CIT p.Val397fs

c.1189del · rs2502433914 · VCV2895340

Pathogenic Single submitter

Classification

Pathogenic

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 in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 10 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.8	GERP 0.39, 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: CIT
Protein: p.Val397fs
Coding: c.1189del
MANE Select: NM_001206999
dbSNP: rs2502433914
Type: Deletion
Location: chr12:119803312 (GRCh38)
Gene constraint: LOEUF 0.353 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.75
Residue 397: the agc-kinase c-terminal domain

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

Similar variants

CIT c.239-9del Likely benign ★★ same type
CIT c.2532-6del Benign/Likely benign ★★ same type
CIT p.Asn10fs Likely pathogenic ★ same type
CIT p.Asp1541fs Pathogenic ★ same type
CIT p.Glu204_Leu205insTer Pathogenic ★ same type
CIT c.753+8del Conflicting classifications of pathogenicity ★ same type
CIT p.Glu225_Val229del Uncertain significance ★ same type
CIT c.1942-105del 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/cit-p-val397fs (accessed [today's date]).

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