Is SYNCRIP p.Phe405fs (c.1215del) pathogenic?

SYNCRIP p.Phe405fs (c.1215del) is classified Uncertain significance in SYNCRIP (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-18). No gnomAD frequency available for this variant.

How common is SYNCRIP p.Phe405fs (c.1215del) in the general population?

SYNCRIP p.Phe405fs (c.1215del) is no gnomAD frequency available for this variant (gnomAD).

SYNCRIP p.Phe405fs

c.1215del · rs2128281759 · VCV1307200

Uncertain significance Single submitter

Classification

Uncertain significance

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 haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 10 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.4, 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: SYNCRIP
Protein: p.Phe405fs
Coding: c.1215del
MANE Select: NM_006372
dbSNP: rs2128281759
Type: Deletion
Location: chr6:85618883 (GRCh38)
Gene constraint: LOEUF 0.249 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 70.83 · 4 PDB
Residue 405: the 'interaction with apobec1' region; the rrm 3 domain; a β-strand

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

Similar variants

SYNCRIP p.Ala299fs Uncertain significance ★ same type
SYNCRIP p.Asp82_Ser83insTer Uncertain significance ★ same type
SYNCRIP p.Gly522fs Uncertain significance ★ same type
SYNCRIP p.Lys284del Uncertain significance ★ same type
SYNCRIP p.Tyr460fs Uncertain significance ★ same type
SYNCRIP p.Val273_Tyr276del 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-phe405fs (accessed [today's date]).

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