Is CIT p.Asn1972= (c.5916C>T) pathogenic?

CIT p.Asn1972= (c.5916C>T) is classified Likely benign in CIT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-31). Very rare (popmax 0.00856%, amr); Associated with CIT-related disorder.

What condition is associated with CIT p.Asn1972= (c.5916C>T)?

CIT p.Asn1972= (c.5916C>T) is associated with CIT-related disorder (ClinVar).

How common is CIT p.Asn1972= (c.5916C>T) in the general population?

CIT p.Asn1972= (c.5916C>T) is very rare (popmax 0.00856%, amr) (gnomAD).

CIT p.Asn1972=

c.5916C>T · rs1301165297 · VCV3044265

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00856%, amr)

Conditions

CIT-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.214	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.86	GERP -3.6
Overall
CADD	6.815	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00856% Admixed American · 5/58,434 alleles

Filtering AF 0.00333% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00211%

Overall 0.000815% 13/1,595,248 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00856%	11,687
Remaining individualsnot grpmax-eligible	0.00322%	31,029
African / African-American	0.00134%	74,732
European (non-Finnish)	0.000425%	235,405

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.Asn1972=
Coding: c.5916C>T
MANE Select: NM_001206999
dbSNP: rs1301165297
Type: single nucleotide variant
Location: chr12:119690421 (GRCh38)
Gene constraint: LOEUF 0.353 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.75
Residue 1972: the 'disordered' region

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.Ile1356= Likely benign same condition
CIT p.Leu1803= 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-asn1972 (accessed [today's date]).

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