Is CD320 p.Val208del (c.622_624del) pathogenic?

CD320 p.Val208del (c.622624del) is classified Uncertain significance in CD320 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-17). Absent from gnomAD; Associated with methylmalonic acidemia due to transcobalamin receptor defect.

What condition is associated with CD320 p.Val208del (c.622_624del)?

CD320 p.Val208del (c.622_624del) is associated with methylmalonic acidemia due to transcobalamin receptor defect (ClinVar).

How common is CD320 p.Val208del (c.622_624del) in the general population?

CD320 p.Val208del (c.622_624del) is absent from gnomAD (gnomAD).

CD320 p.Val208del

c.622_624del · rs2512594697 · VCV2017815

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

methylmalonic acidemia due to transcobalamin receptor defect

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 -1.3	GERP -1.4, phastCons 0.003
Region caveats
Repeat context	tandem	TGTGGCATTCCCGACAGAGGGGACACTCTCCAGGGTCACAGGGGGCCCCATGGT simple repeat · ambiguous alignment · confidence, not pathogenicity

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: CD320
Protein: p.Val208del
Coding: c.622_624del
MANE Select: NM_016579
dbSNP: rs2512594697
Type: Deletion
Location: chr19:8302859 (GRCh38)
Gene constraint: LOEUF 1.488 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.61 · 6 PDB
Residue 208: the 'disordered' region

Full CD320 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

methylmalonic acidemia due to transcobalamin receptor defect — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD320 p.Val208_Pro209insThrSerLeuArgAsnAlaThrThrMetGlyProProValThrLeuGluSerVal Uncertain significance ★ same residue
CD320 p.Leu66fs Uncertain significance ★ same condition
CD320 p.Thr191_Val208del Uncertain significance ★ same condition
CD320 c.707-19_707-18del Likely benign ★ same condition
CD320 p.Arg129Leu Uncertain significance ★★ ⚠ same condition
CD320 p.Arg138Ser Uncertain significance ★★ ⚠ same condition
CD320 p.Arg254Gln Uncertain significance ★★ ⚠ same condition
CD320 p.Arg258His 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/cd320-p-val208del (accessed [today's date]).

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