Is TDRD9 p.Pro48= (c.144C>T) pathogenic?

TDRD9 p.Pro48= (c.144C>T) is classified Likely benign in TDRD9 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-20). No allele count reported in gnomAD v4.1 (AN 1,249,684); Associated with TDRD9-related disorder.

What condition is associated with TDRD9 p.Pro48= (c.144C>T)?

TDRD9 p.Pro48= (c.144C>T) is associated with TDRD9-related disorder (ClinVar).

How common is TDRD9 p.Pro48= (c.144C>T) in the general population?

TDRD9 p.Pro48= (c.144C>T) is no allele count reported in gnomAD v4.1 (AN 1,249,684) (gnomAD).

TDRD9 p.Pro48=

c.144C>T · rs867213957 · VCV3045991

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,249,684)

Conditions

TDRD9-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5	GERP -2
Overall
CADD	4.133	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,249,684). 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: TDRD9
Protein: p.Pro48=
Coding: c.144C>T
MANE Select: NM_153046
dbSNP: rs867213957
Type: single nucleotide variant
Location: chr14:103928653 (GRCh38)
Gene constraint: LOEUF 0.893 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.45
Residue 48: the 'disordered' region

Full TDRD9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

TDRD9-related disorder

Similar variants

TDRD9 c.2223+3G>A Likely benign same condition
TDRD9 c.2607-5T>C Benign same condition
TDRD9 c.2719-5T>G Likely benign same condition
TDRD9 c.3975-7A>T Likely benign same condition
TDRD9 c.421-3T>C Likely benign same condition
TDRD9 c.642+8T>G Likely benign same condition
TDRD9 c.*1G>A Benign same condition
TDRD9 p.Ala1319= Likely benign 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/tdrd9-p-pro48 (accessed [today's date]).

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