Is CD96 p.Asp312fs (c.934del) pathogenic?

CD96 p.Asp312fs (c.934del) is classified Uncertain significance in CD96 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-04-28). No gnomAD frequency available for this variant; Associated with C syndrome.

What condition is associated with CD96 p.Asp312fs (c.934del)?

CD96 p.Asp312fs (c.934del) is associated with C syndrome (ClinVar).

How common is CD96 p.Asp312fs (c.934del) in the general population?

CD96 p.Asp312fs (c.934del) is no gnomAD frequency available for this variant (gnomAD).

CD96 p.Asp312fs

c.934del · rs1937457440 · VCV1199409

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

C syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 7 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.3	GERP 0.43, phastCons 0.066

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: CD96
Protein: p.Asp312fs
Coding: c.934del
MANE Select: NM_005816
dbSNP: rs1937457440
Type: Deletion
Location: chr3:111600761 (GRCh38)
Gene constraint: LOEUF 1.16 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.81 · 1 PDB
Residue 312: the ig-like c2-type domain

Full CD96 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

C syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD96 c.544-1477_544-1459del Uncertain significance ★ same condition
CD96 p.Asp312Gly Likely benign ★ same residue
CD96 p.Trp179fs Likely pathogenic same condition
CD96 c.1249+1G>A Uncertain significance ★★ same condition
CD96 c.807+14A>C Benign/Likely benign ★★ same condition
CD96 c.1321+1G>A Likely pathogenic ★ same condition
CD96 c.807+2T>A Likely pathogenic ★ same condition
CD96 c.1181-12T>C Uncertain significance ★ 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/cd96-p-asp312fs (accessed [today's date]).

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