Is CIT p.Leu1803= (c.5409C>A) pathogenic?

CIT p.Leu1803= (c.5409C>A) is classified Likely benign in CIT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-11). Ultra-rare (popmax 0.0107%, afr); Associated with CIT-related disorder.

What condition is associated with CIT p.Leu1803= (c.5409C>A)?

CIT p.Leu1803= (c.5409C>A) is associated with CIT-related disorder (ClinVar).

How common is CIT p.Leu1803= (c.5409C>A) in the general population?

CIT p.Leu1803= (c.5409C>A) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

CIT p.Leu1803=

c.5409C>A · rs779034565 · VCV3050055

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Conditions

CIT-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 -9.2	GERP -3.9
Overall
CADD	0.017	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/74,916 alleles

Filtering AF 0.00528% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.00118% 19/1,613,830 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,365
European (non-Finnish)	0.000932%	107,257

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: CIT
Protein: p.Leu1803=
Coding: c.5409C>A
MANE Select: NM_001206999
dbSNP: rs779034565
Type: single nucleotide variant
Location: chr12:119701854 (GRCh38)
Gene constraint: LOEUF 0.353 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.75
Residue 1803: the cnh domain

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

Disease context

CIT-related disorder

Similar variants

CIT p.Gln64Ter Likely pathogenic ★ same condition
CIT c.2532-9C>T Likely benign same condition
CIT c.3486+7G>A Likely benign same condition
CIT c.6187-4C>T Likely benign same condition
CIT p.Asn1972= Likely benign same condition
CIT p.Ile1356= Likely benign same condition
CIT p.Pro1377= Likely benign same condition
CIT p.Pro1717= Likely 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/cit-p-leu1803 (accessed [today's date]).

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