Is SNRNP200 p.Ile1663del (c.4986CAT[1]) pathogenic?

SNRNP200 p.Ile1663del (c.4986CAT[1]) is classified Uncertain significance in SNRNP200 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-06). Very rare (popmax 0.000169%, nfe).

How common is SNRNP200 p.Ile1663del (c.4986CAT[1]) in the general population?

SNRNP200 p.Ile1663del (c.4986CAT[1]) is very rare (popmax 0.000169%, nfe) (gnomAD).

SNRNP200 p.Ile1663del

c.4986CAT[1] · rs1434410149 · VCV2002516

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 1.9, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000169% European (non-Finnish) · 2/1,179,958 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000186% 3/1,614,070 alleles · very rare exomes 3/1,461,788 · genomes 0/152,282 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0016%	62,498
European (non-Finnish)grpmax	0.000169%	589,977

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: SNRNP200
Protein: p.Ile1663del
Coding: c.4986CAT[1]
MANE Select: NM_014014
dbSNP: rs1434410149
Type: Microsatellite
Location: chr2:96281847 (GRCh38)
Gene constraint: LOEUF 0.312 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.89 · 85 PDB
Residue 1663: a β-strand; the helicase c-terminal 2 domain; the 'interaction with c9orf78 and wbp4' region; the 'interaction with tssc4' region

Full SNRNP200 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SNRNP200 p.Ile1663Val Conflicting classifications of pathogenicity ★ ⚠ same residue
SNRNP200 p.Ile1663Thr Likely benign ★ same residue
SNRNP200 c.1376_1377+1del Uncertain significance ★ same type
SNRNP200 c.5324-12_5324-11del Uncertain significance ★ same type
SNRNP200 p.Asp942del Uncertain significance ★ same type
SNRNP200 p.Glu579del Uncertain significance ★ same type
SNRNP200 p.His573del Uncertain significance ★ same type
SNRNP200 p.Lys256del 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/snrnp200-p-ile1663del (accessed [today's date]).

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