Is SYNCRIP p.Tyr456Ter (c.1368T>G) pathogenic?

SYNCRIP p.Tyr456Ter (c.1368T>G) is classified Uncertain significance in SYNCRIP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-22). Absent from gnomAD v4.1; Associated with SYNCRIP-related neurodevelopmental disorder.

What condition is associated with SYNCRIP p.Tyr456Ter (c.1368T>G)?

SYNCRIP p.Tyr456Ter (c.1368T>G) is associated with SYNCRIP-related neurodevelopmental disorder (ClinVar).

How common is SYNCRIP p.Tyr456Ter (c.1368T>G) in the general population?

SYNCRIP p.Tyr456Ter (c.1368T>G) is absent from gnomAD v4.1 (gnomAD).

SYNCRIP p.Tyr456Ter

c.1368T>G · rs2128278447 · VCV1526182

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

SYNCRIP-related neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (11 of 11) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP -0.23, phastCons 1
Overall
CADD	39.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SYNCRIP
Protein: p.Tyr456Ter
Coding: c.1368T>G
MANE Select: NM_006372
dbSNP: rs2128278447
Type: single nucleotide variant
Location: chr6:85615260 (GRCh38)
Gene constraint: LOEUF 0.249 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 70.83 · 4 PDB
Residue 456: the 'interaction with apobec1' region; the '8 x 3 aa repeats of r-g-g' region

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

Disease context

SYNCRIP-related neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SYNCRIP p.Ala374Glu Uncertain significance ★ ⚠ same condition
SYNCRIP p.Gly505Val Uncertain significance ★ ⚠ same condition
SYNCRIP p.Pro437Ser Uncertain significance ★ ⚠ same condition
SYNCRIP p.Gln492fs Pathogenic ★ same condition
SYNCRIP p.Ala216Thr Uncertain significance ★★ same type
SYNCRIP p.Asn243Ser Uncertain significance ★★ ⚠ same type
SYNCRIP p.Pro440Leu Uncertain significance ★★ ⚠ same type
SYNCRIP p.Pro508Leu 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/syncrip-p-tyr456ter (accessed [today's date]).

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